rs201000269
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006307.5(SRPX):c.769G>C(p.Val257Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000173 in 1,207,793 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 64 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006307.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPX | ENST00000378533.4 | c.769G>C | p.Val257Leu | missense_variant | Exon 6 of 10 | 1 | NM_006307.5 | ENSP00000367794.3 | ||
ENSG00000250349 | ENST00000465127.1 | c.172-505182C>G | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 |
Frequencies
GnomAD3 genomes AF: 0.0000895 AC: 10AN: 111723Hom.: 0 Cov.: 22 AF XY: 0.0000295 AC XY: 1AN XY: 33897
GnomAD3 exomes AF: 0.0000657 AC: 12AN: 182683Hom.: 0 AF XY: 0.0000893 AC XY: 6AN XY: 67161
GnomAD4 exome AF: 0.000182 AC: 199AN: 1096016Hom.: 0 Cov.: 29 AF XY: 0.000174 AC XY: 63AN XY: 361474
GnomAD4 genome AF: 0.0000895 AC: 10AN: 111777Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 33961
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.769G>C (p.V257L) alteration is located in exon 6 (coding exon 6) of the SRPX gene. This alteration results from a G to C substitution at nucleotide position 769, causing the valine (V) at amino acid position 257 to be replaced by a leucine (L). 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