11-126266580-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_003139.4(SRPRA):c.736C>T(p.Arg246Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003139.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRPRA | NM_003139.4 | c.736C>T | p.Arg246Trp | missense_variant | Exon 6 of 14 | ENST00000332118.11 | NP_003130.2 | |
SRPRA | NM_001177842.2 | c.652C>T | p.Arg218Trp | missense_variant | Exon 5 of 13 | NP_001171313.1 | ||
SRPRA | XM_047427497.1 | c.736C>T | p.Arg246Trp | missense_variant | Exon 6 of 14 | XP_047283453.1 | ||
SRPRA | XM_017018179.3 | c.736C>T | p.Arg246Trp | missense_variant | Exon 6 of 14 | XP_016873668.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPRA | ENST00000332118.11 | c.736C>T | p.Arg246Trp | missense_variant | Exon 6 of 14 | 1 | NM_003139.4 | ENSP00000328023.5 | ||
SRPRA | ENST00000532259.1 | c.652C>T | p.Arg218Trp | missense_variant | Exon 5 of 13 | 2 | ENSP00000435508.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249062Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134822
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.736C>T (p.R246W) alteration is located in exon 6 (coding exon 6) of the SRPRA gene. This alteration results from a C to T substitution at nucleotide position 736, causing the arginine (R) at amino acid position 246 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at