chr3-46408581-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003965.5(CCRL2):c.502G>A(p.Val168Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,614,014 control chromosomes in the GnomAD database, including 16,150 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_003965.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCRL2 | NM_003965.5 | c.502G>A | p.Val168Met | missense_variant | Exon 2 of 2 | ENST00000399036.4 | NP_003956.2 | |
CCRL2 | NM_001130910.2 | c.538G>A | p.Val180Met | missense_variant | Exon 2 of 2 | NP_001124382.1 | ||
CCRL2 | XM_011534208.2 | c.502G>A | p.Val168Met | missense_variant | Exon 3 of 3 | XP_011532510.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.122 AC: 18589AN: 152160Hom.: 1286 Cov.: 33
GnomAD3 exomes AF: 0.110 AC: 27379AN: 249432Hom.: 1923 AF XY: 0.107 AC XY: 14445AN XY: 135330
GnomAD4 exome AF: 0.136 AC: 198770AN: 1461736Hom.: 14863 Cov.: 36 AF XY: 0.132 AC XY: 96264AN XY: 727158
GnomAD4 genome AF: 0.122 AC: 18608AN: 152278Hom.: 1287 Cov.: 33 AF XY: 0.118 AC XY: 8809AN XY: 74468
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at