X-38160972-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006307.5(SRPX):āc.736G>Cā(p.Glu246Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000157 in 1,208,012 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPX | ENST00000378533.4 | c.736G>C | p.Glu246Gln | missense_variant | Exon 6 of 10 | 1 | NM_006307.5 | ENSP00000367794.3 | ||
ENSG00000250349 | ENST00000465127.1 | c.172-505149C>G | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 |
Frequencies
GnomAD3 genomes AF: 0.0000628 AC: 7AN: 111488Hom.: 0 Cov.: 22 AF XY: 0.0000594 AC XY: 2AN XY: 33680
GnomAD3 exomes AF: 0.0000328 AC: 6AN: 183019Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67483
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1096524Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 1AN XY: 361972
GnomAD4 genome AF: 0.0000628 AC: 7AN: 111488Hom.: 0 Cov.: 22 AF XY: 0.0000594 AC XY: 2AN XY: 33680
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.736G>C (p.E246Q) 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 736, causing the glutamic acid (E) at amino acid position 246 to be replaced by a glutamine (Q). 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