rs192329378
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000258.3(MYL3):c.130-14G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00247 in 1,613,968 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000258.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYL3 | NM_000258.3 | c.130-14G>T | intron_variant | Intron 1 of 6 | ENST00000292327.6 | NP_000249.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00195 AC: 296AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00161 AC: 404AN: 250952Hom.: 0 AF XY: 0.00172 AC XY: 234AN XY: 135692
GnomAD4 exome AF: 0.00252 AC: 3686AN: 1461740Hom.: 4 Cov.: 33 AF XY: 0.00249 AC XY: 1812AN XY: 727140
GnomAD4 genome AF: 0.00194 AC: 296AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00207 AC XY: 154AN XY: 74432
ClinVar
Submissions by phenotype
Hypertrophic cardiomyopathy 8 Benign:6
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
not provided Benign:3
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not specified Benign:2
130-14G>T in intron 01 of MYL3: This variant is not expected to have clinical si gnificance because it has been identified in 0.4% (31/7020) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS/). 130-14G>T in intron 01 of MYL3 (allele frequenc y = 0.4%, 31/7020) ** -
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Hypertrophic cardiomyopathy Benign:2
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Cardiomyopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at