3-108383733-T-TAAAAACAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_014981.3(MYH15):​c.5632-5_5632-4insTTTTTTTTTTTTGTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 29)

Consequence

MYH15
NM_014981.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240
Variant links:
Genes affected
MYH15 (HGNC:31073): (myosin heavy chain 15) Predicted to enable several functions, including ATP binding activity; actin filament binding activity; and calmodulin binding activity. Predicted to be involved in extraocular skeletal muscle development. Located in cytosol and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MYH15NM_014981.3 linkc.5632-5_5632-4insTTTTTTTTTTTTGTTTTT splice_region_variant, intron_variant Intron 39 of 40 ENST00000693548.1 NP_055796.2 Q9Y2K3
MYH15XM_011512559.3 linkc.5692-5_5692-4insTTTTTTTTTTTTGTTTTT splice_region_variant, intron_variant Intron 41 of 42 XP_011510861.1 Q9Y2K3
LOC124900545XR_007095998.1 linkn.112+2087_112+2088insCAAAAAAAAAAAAAAAAA intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYH15ENST00000693548.1 linkc.5632-5_5632-4insTTTTTTTTTTTTGTTTTT splice_region_variant, intron_variant Intron 39 of 40 NM_014981.3 ENSP00000508967.1 A0A8I5KXJ3
MYH15ENST00000273353.5 linkc.5632-5_5632-4insTTTTTTTTTTTTGTTTTT splice_region_variant, intron_variant Intron 40 of 41 1 ENSP00000273353.4 Q9Y2K3
MYH15ENST00000689784.1 linkc.4651-5_4651-4insTTTTTTTTTTTTGTTTTT splice_region_variant, intron_variant Intron 31 of 32 ENSP00000509841.1 A0A8I5KYE8

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs377049870; hg19: chr3-108102580; API