11-829393-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001286606.2(CRACR2B):c.311C>A(p.Ala104Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000832 in 1,610,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001286606.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRACR2B | ENST00000525077.2 | c.311C>A | p.Ala104Glu | missense_variant | Exon 3 of 9 | 1 | NM_001286606.2 | ENSP00000435299.1 | ||
CRACR2B | ENST00000528542.6 | c.311C>A | p.Ala104Glu | missense_variant | Exon 4 of 9 | 1 | ENSP00000432334.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152220Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000827 AC: 20AN: 241852Hom.: 0 AF XY: 0.0000984 AC XY: 13AN XY: 132080
GnomAD4 exome AF: 0.0000885 AC: 129AN: 1457780Hom.: 0 Cov.: 32 AF XY: 0.000112 AC XY: 81AN XY: 725078
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152338Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.311C>A (p.A104E) alteration is located in exon 4 (coding exon 3) of the CRACR2B gene. This alteration results from a C to A substitution at nucleotide position 311, causing the alanine (A) at amino acid position 104 to be replaced by a glutamic acid (E). 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