X-38160138-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006307.5(SRPX):c.834C>T(p.Asp278Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000033 in 1,210,350 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006307.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRPX | ENST00000378533.4 | c.834C>T | p.Asp278Asp | synonymous_variant | Exon 7 of 10 | 1 | NM_006307.5 | ENSP00000367794.3 | ||
ENSG00000250349 | ENST00000465127.1 | c.172-505983G>A | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 |
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112335Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1AN XY: 34509
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182838Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67342
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1098015Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363373
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112335Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1AN XY: 34509
ClinVar
Submissions by phenotype
not provided Benign:1
SRPX: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at