X-38160076-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006307.5(SRPX):c.896G>T(p.Ser299Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000992 in 1,210,174 control chromosomes in the GnomAD database, including 1 homozygotes. There are 31 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPX | ENST00000378533.4 | c.896G>T | p.Ser299Ile | missense_variant | Exon 7 of 10 | 1 | NM_006307.5 | ENSP00000367794.3 | ||
ENSG00000250349 | ENST00000465127.1 | c.172-506045C>A | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 |
Frequencies
GnomAD3 genomes AF: 0.000382 AC: 43AN: 112613Hom.: 0 Cov.: 23 AF XY: 0.000173 AC XY: 6AN XY: 34745
GnomAD3 exomes AF: 0.000183 AC: 33AN: 180246Hom.: 0 AF XY: 0.000108 AC XY: 7AN XY: 65032
GnomAD4 exome AF: 0.0000702 AC: 77AN: 1097508Hom.: 1 Cov.: 31 AF XY: 0.0000689 AC XY: 25AN XY: 362930
GnomAD4 genome AF: 0.000382 AC: 43AN: 112666Hom.: 0 Cov.: 23 AF XY: 0.000172 AC XY: 6AN XY: 34808
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.896G>T (p.S299I) alteration is located in exon 7 (coding exon 7) of the SRPX gene. This alteration results from a G to T substitution at nucleotide position 896, causing the serine (S) at amino acid position 299 to be replaced by an isoleucine (I). 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