ClinVar Miner

Submissions for variant NM_003482.4(KMT2D):c.14643+3A>T

gnomAD frequency: 0.00011  dbSNP: rs374232950
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001568238 SCV001792078 likely benign not provided 2020-04-16 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV001568238 SCV003812662 uncertain significance not provided 2021-08-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003588746 SCV004269875 uncertain significance Kabuki syndrome 2024-10-21 criteria provided, single submitter clinical testing This sequence change falls in intron 47 of the KMT2D gene. It does not directly change the encoded amino acid sequence of the KMT2D protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs374232950, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with KMT2D-related conditions. ClinVar contains an entry for this variant (Variation ID: 1202526). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV005005968 SCV005636779 likely benign Kabuki syndrome 1; Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome 2024-04-25 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004542015 SCV004791220 likely benign KMT2D-related disorder 2021-08-31 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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