12-57047383-T-TAAG

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting

The NM_005379.4(MYO1A):​c.349_350insCTT​(p.Ser116dup) variant causes a inframe insertion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

MYO1A
NM_005379.4 inframe_insertion

Scores

Not classified

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 7.42
Variant links:
Genes affected
MYO1A (HGNC:7595): (myosin IA) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional skeletal muscle myosin-1 (MYH1). Unconventional myosins contain the basic domains characteristic of conventional myosins and are further distinguished from class members by their tail domains. They function as actin-based molecular motors. Mutations in this gene have been associated with autosomal dominant deafness. Alternatively spliced variants have been found for this gene. [provided by RefSeq, Dec 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_005379.4. Strenght limited to Supporting due to length of the change: 1aa.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYO1ANM_005379.4 linkuse as main transcriptc.349_350insCTT p.Ser116dup inframe_insertion 5/28 ENST00000300119.8 NP_005370.1
MYO1ANM_001256041.2 linkuse as main transcriptc.349_350insCTT p.Ser116dup inframe_insertion 6/29 NP_001242970.1
MYO1AXM_011538373.3 linkuse as main transcriptc.349_350insCTT p.Ser116dup inframe_insertion 5/25 XP_011536675.1
MYO1AXM_047428876.1 linkuse as main transcriptc.349_350insCTT p.Ser116dup inframe_insertion 6/29 XP_047284832.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MYO1AENST00000300119.8 linkuse as main transcriptc.349_350insCTT p.Ser116dup inframe_insertion 5/281 NM_005379.4 ENSP00000300119 P1
MYO1AENST00000442789.6 linkuse as main transcriptc.349_350insCTT p.Ser116dup inframe_insertion 6/291 ENSP00000393392 P1
MYO1AENST00000492945.5 linkuse as main transcriptc.-21+2503_-21+2504insCTT intron_variant 4 ENSP00000452229
MYO1AENST00000554234.5 linkuse as main transcriptc.-91_-90insCTT 5_prime_UTR_variant, NMD_transcript_variant 2/245 ENSP00000451033

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Autosomal dominant nonsyndromic hearing loss 48 Uncertain:1
Uncertain significance, no assertion criteria providedliterature onlyOMIMMay 01, 2014- -

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: rs864309476; hg19: chr12-57441167; API