rs111033507
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_000260.4(MYO7A):c.3042G>A(p.Thr1014=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,208 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T1014T) has been classified as Likely benign.
Frequency
Consequence
NM_000260.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO7A | NM_000260.4 | c.3042G>A | p.Thr1014= | synonymous_variant | 24/49 | ENST00000409709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO7A | ENST00000409709.9 | c.3042G>A | p.Thr1014= | synonymous_variant | 24/49 | 1 | NM_000260.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152066Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248452Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135094
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461142Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 726848
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152066Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74270
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 08, 2023 | - - |
MYO7A-related condition Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at