rs201705384
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005379.4(MYO1A):c.771G>A(p.Ser257=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,614,134 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
MYO1A
NM_005379.4 synonymous
NM_005379.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.00
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 12-57043977-C-T is Benign according to our data. Variant chr12-57043977-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 164596.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2 with no splicing effect.
BS2
?
High AC in GnomAd4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO1A | NM_005379.4 | c.771G>A | p.Ser257= | synonymous_variant | 10/28 | ENST00000300119.8 | |
MYO1A | NM_001256041.2 | c.771G>A | p.Ser257= | synonymous_variant | 11/29 | ||
MYO1A | XM_047428876.1 | c.771G>A | p.Ser257= | synonymous_variant | 11/29 | ||
MYO1A | XM_011538373.3 | c.771G>A | p.Ser257= | synonymous_variant | 10/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1A | ENST00000300119.8 | c.771G>A | p.Ser257= | synonymous_variant | 10/28 | 1 | NM_005379.4 | P1 | |
MYO1A | ENST00000442789.6 | c.771G>A | p.Ser257= | synonymous_variant | 11/29 | 1 | P1 | ||
MYO1A | ENST00000492945.5 | c.-20-619G>A | intron_variant | 4 | |||||
MYO1A | ENST00000554234.5 | c.285G>A | p.Ser95= | synonymous_variant, NMD_transcript_variant | 6/24 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152128Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
10
AN:
152128
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251250Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135780
GnomAD3 exomes
AF:
AC:
8
AN:
251250
Hom.:
AF XY:
AC XY:
5
AN XY:
135780
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727244
GnomAD4 exome
AF:
AC:
26
AN:
1461888
Hom.:
Cov.:
32
AF XY:
AC XY:
12
AN XY:
727244
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74428
GnomAD4 genome
?
AF:
AC:
12
AN:
152246
Hom.:
Cov.:
32
AF XY:
AC XY:
6
AN XY:
74428
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 13, 2014 | Ser257Ser in Exon 10 of MYO1A: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 1% (2/192) Kenyan chr omosomes by the 1000 Genomes Project (http://www.1000genomes.org; dbSNP rs201705 384). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at