chr5-140550722-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001035235.4(SRA1):c.653C>T(p.Pro218Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000825 in 1,614,026 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001035235.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRA1 | NM_001035235.4 | c.653C>T | p.Pro218Leu | missense_variant | 5/5 | ENST00000336283.9 | |
SRA1 | NM_001253764.2 | c.605C>T | p.Pro202Leu | missense_variant | 3/3 | ||
SRA1 | NR_045586.1 | n.1354C>T | non_coding_transcript_exon_variant | 5/5 | |||
SRA1 | NR_045587.2 | n.829C>T | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRA1 | ENST00000336283.9 | c.653C>T | p.Pro218Leu | missense_variant | 5/5 | 1 | NM_001035235.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00451 AC: 685AN: 152024Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00121 AC: 303AN: 251434Hom.: 1 AF XY: 0.000957 AC XY: 130AN XY: 135902
GnomAD4 exome AF: 0.000443 AC: 647AN: 1461884Hom.: 2 Cov.: 31 AF XY: 0.000410 AC XY: 298AN XY: 727242
GnomAD4 genome ? AF: 0.00450 AC: 685AN: 152142Hom.: 3 Cov.: 32 AF XY: 0.00433 AC XY: 322AN XY: 74382
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
SRA1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 09, 2019 | This variant is classified as 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