rs146497334
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_033118.4(MYLK2):c.1778C>T(p.Ala593Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000738 in 1,613,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_033118.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYLK2 | ENST00000375985.5 | c.1778C>T | p.Ala593Val | missense_variant | Exon 13 of 13 | 1 | NM_033118.4 | ENSP00000365152.4 | ||
MYLK2 | ENST00000375994.6 | c.1778C>T | p.Ala593Val | missense_variant | Exon 12 of 12 | 1 | ENSP00000365162.2 | |||
MYLK2 | ENST00000468730.1 | n.716C>T | non_coding_transcript_exon_variant | Exon 6 of 6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000473 AC: 72AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000920 AC: 23AN: 250112Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135334
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1460728Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 726714
GnomAD4 genome AF: 0.000473 AC: 72AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000483 AC XY: 36AN XY: 74472
ClinVar
Submissions by phenotype
Hypertrophic cardiomyopathy 1 Uncertain:1Benign:1
ACMG classification criteria: BP4 supporting -
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not specified Benign:2
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The p.Ala593Val variant in MYLK2 is classified as benign because it has been identified in 0.16% (41/24934) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BA1. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at