chrX-38160034-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_006307.5(SRPX):c.938C>T(p.Thr313Met) variant causes a missense change. The variant allele was found at a frequency of 0.000107 in 1,209,442 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 43 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006307.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPX | ENST00000378533.4 | c.938C>T | p.Thr313Met | missense_variant | Exon 7 of 10 | 1 | NM_006307.5 | ENSP00000367794.3 | ||
ENSG00000250349 | ENST00000465127.1 | c.172-506087G>A | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 |
Frequencies
GnomAD3 genomes AF: 0.000133 AC: 15AN: 112568Hom.: 0 Cov.: 23 AF XY: 0.000115 AC XY: 4AN XY: 34702
GnomAD3 exomes AF: 0.000136 AC: 24AN: 176987Hom.: 0 AF XY: 0.000128 AC XY: 8AN XY: 62267
GnomAD4 exome AF: 0.000105 AC: 115AN: 1096820Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 39AN XY: 362318
GnomAD4 genome AF: 0.000133 AC: 15AN: 112622Hom.: 0 Cov.: 23 AF XY: 0.000115 AC XY: 4AN XY: 34766
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.938C>T (p.T313M) alteration is located in exon 7 (coding exon 7) of the SRPX gene. This alteration results from a C to T substitution at nucleotide position 938, causing the threonine (T) at amino acid position 313 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Benign:1
SRPX: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at