11-126266516-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003139.4(SRPRA):āc.800A>Gā(p.Asn267Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,614,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.800A>G | p.Asn267Ser | missense_variant | Exon 6 of 14 | ENST00000332118.11 | NP_003130.2 | |
SRPRA | NM_001177842.2 | c.716A>G | p.Asn239Ser | missense_variant | Exon 5 of 13 | NP_001171313.1 | ||
SRPRA | XM_047427497.1 | c.800A>G | p.Asn267Ser | missense_variant | Exon 6 of 14 | XP_047283453.1 | ||
SRPRA | XM_017018179.3 | c.800A>G | p.Asn267Ser | 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.800A>G | p.Asn267Ser | missense_variant | Exon 6 of 14 | 1 | NM_003139.4 | ENSP00000328023.5 | ||
SRPRA | ENST00000532259.1 | c.716A>G | p.Asn239Ser | missense_variant | Exon 5 of 13 | 2 | ENSP00000435508.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249106Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134852
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461862Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727236
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.800A>G (p.N267S) alteration is located in exon 6 (coding exon 6) of the SRPRA gene. This alteration results from a A to G substitution at nucleotide position 800, causing the asparagine (N) at amino acid position 267 to be replaced by a serine (S). 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