11-126265108-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_003139.4(SRPRA):c.1376C>T(p.Ala459Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,006 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRPRA | NM_003139.4 | c.1376C>T | p.Ala459Val | missense_variant | Exon 11 of 14 | ENST00000332118.11 | NP_003130.2 | |
SRPRA | NM_001177842.2 | c.1292C>T | p.Ala431Val | missense_variant | Exon 10 of 13 | NP_001171313.1 | ||
SRPRA | XM_047427497.1 | c.1376C>T | p.Ala459Val | missense_variant | Exon 11 of 14 | XP_047283453.1 | ||
SRPRA | XM_017018179.3 | c.1376C>T | p.Ala459Val | missense_variant | Exon 11 of 14 | XP_016873668.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPRA | ENST00000332118.11 | c.1376C>T | p.Ala459Val | missense_variant | Exon 11 of 14 | 1 | NM_003139.4 | ENSP00000328023.5 | ||
SRPRA | ENST00000532259.1 | c.1292C>T | p.Ala431Val | missense_variant | Exon 10 of 13 | 2 | ENSP00000435508.1 | |||
SRPRA | ENST00000527817.1 | n.659C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 2 | |||||
SRPRA | ENST00000531104.1 | n.455C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251350Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135874
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727238
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1376C>T (p.A459V) alteration is located in exon 11 (coding exon 11) of the SRPRA gene. This alteration results from a C to T substitution at nucleotide position 1376, causing the alanine (A) at amino acid position 459 to be replaced by a valine (V). 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