rs9332739
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM2_SupportingBP4_StrongBP7
The NM_000063(C2):c.954G>A(p.Glu318=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
C2
NM_000063 synonymous
NM_000063 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.346
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 31.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP7
?
Synonymous conserved (PhyloP=0.346 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C2 | NM_000063.6 | c.954G>A | p.Glu318= | synonymous_variant | 7/18 | ENST00000299367.10 | |
C2-AS1 | NR_104191.1 | n.541-625C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C2 | ENST00000299367.10 | c.954G>A | p.Glu318= | synonymous_variant | 7/18 | 1 | NM_000063.6 | P1 | |
C2-AS1 | ENST00000630806.1 | n.541-625C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomesCov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246608Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134420
GnomAD3 exomes
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460754Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 726692
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at