X-38160939-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006307.5(SRPX):āc.769G>Cā(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 (ā ).
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