ClinVar Miner

Submissions for variant NM_194292.3(SASS6):c.1057-6_1057-2del

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology RCV002465006 SCV002759398 likely pathogenic Microcephaly 14, primary, autosomal recessive 2022-06-21 criteria provided, single submitter clinical testing The c.1057-6_1057-2del variant is not present in publicly available population databases like 1000 Genomes, Exome Variant Server (EVS) and Indian Exome Database. The heterozygous state of the variant is present in Genome Aggregation Database (gnomAD), at a low frequency. The variant is not present in our in-house exome database. The variant was not reported to ClinVar, Human Genome Mutation Database (HGMD) and/or OMIM databases in any affected individuals. In-silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome etc. predicted this variant to be likely deleterious. The intronic variant is located within ±2 of splice-site and expected to affect splicing of mRNA.
Ambry Genetics RCV002571380 SCV003727168 uncertain significance Inborn genetic diseases 2021-01-13 criteria provided, single submitter clinical testing The c.1057-6_1057-2delTATCA alteration is located in intron 9 of the SASS6 gene. This alteration consists of a deletion of 5 nucleotides at nucleotide position c.1057-6_1057-2. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Neuberg Centre For Genomic Medicine, NCGM RCV002465006 SCV004047365 likely pathogenic Microcephaly 14, primary, autosomal recessive criteria provided, single submitter clinical testing The splice acceptor c.1057-6_1057-2del- variant has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant has allele frequency of 0.024% in the gnomad and novel (not in any individuals) in 1000 genome database. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.

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