rs971756
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001142620.2(STRA6):c.454T>A(p.Leu152Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,543,242 control chromosomes in the GnomAD database, including 30,271 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001142620.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STRA6 | NM_022369.4 | c.430+24T>A | intron_variant | ENST00000395105.9 | NP_071764.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STRA6 | ENST00000395105.9 | c.430+24T>A | intron_variant | 1 | NM_022369.4 | ENSP00000378537.4 |
Frequencies
GnomAD3 genomes AF: 0.139 AC: 21038AN: 151704Hom.: 2026 Cov.: 32
GnomAD3 exomes AF: 0.138 AC: 21697AN: 156878Hom.: 2111 AF XY: 0.136 AC XY: 11240AN XY: 82544
GnomAD4 exome AF: 0.190 AC: 263920AN: 1391420Hom.: 28245 Cov.: 29 AF XY: 0.185 AC XY: 127364AN XY: 686706
GnomAD4 genome AF: 0.139 AC: 21034AN: 151822Hom.: 2026 Cov.: 32 AF XY: 0.137 AC XY: 10125AN XY: 74172
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at