11-126266778-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003139.4(SRPRA):c.671G>A(p.Gly224Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,613,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRPRA | NM_003139.4 | c.671G>A | p.Gly224Asp | missense_variant | Exon 5 of 14 | ENST00000332118.11 | NP_003130.2 | |
SRPRA | NM_001177842.2 | c.587G>A | p.Gly196Asp | missense_variant | Exon 4 of 13 | NP_001171313.1 | ||
SRPRA | XM_047427497.1 | c.671G>A | p.Gly224Asp | missense_variant | Exon 5 of 14 | XP_047283453.1 | ||
SRPRA | XM_017018179.3 | c.671G>A | p.Gly224Asp | missense_variant | Exon 5 of 14 | XP_016873668.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPRA | ENST00000332118.11 | c.671G>A | p.Gly224Asp | missense_variant | Exon 5 of 14 | 1 | NM_003139.4 | ENSP00000328023.5 | ||
SRPRA | ENST00000532259.1 | c.587G>A | p.Gly196Asp | missense_variant | Exon 4 of 13 | 2 | ENSP00000435508.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461824Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727202
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74330
ClinVar
Submissions by phenotype
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at