chrX-38160141-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006307.5(SRPX):c.831C>A(p.Ser277Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000165 in 1,210,370 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPX | ENST00000378533.4 | c.831C>A | p.Ser277Arg | missense_variant | Exon 7 of 10 | 1 | NM_006307.5 | ENSP00000367794.3 | ||
ENSG00000250349 | ENST00000465127.1 | c.172-505980G>T | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 |
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112339Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34487
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182926Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67436
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098031Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363389
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112339Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34487
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.831C>A (p.S277R) alteration is located in exon 7 (coding exon 7) of the SRPX gene. This alteration results from a C to A substitution at nucleotide position 831, causing the serine (S) at amino acid position 277 to be replaced by an arginine (R). 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