rs17616
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001006658.3(CR2):c.2012G>A(p.Arg671His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 1,611,296 control chromosomes in the GnomAD database, including 76,008 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R671C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001006658.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CR2 | NM_001006658.3 | c.2012G>A | p.Arg671His | missense_variant | 11/20 | ENST00000367057.8 | |
CR2 | NM_001877.5 | c.1979-223G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CR2 | ENST00000367057.8 | c.2012G>A | p.Arg671His | missense_variant | 11/20 | 1 | NM_001006658.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.301 AC: 45751AN: 151956Hom.: 7219 Cov.: 32
GnomAD3 exomes AF: 0.260 AC: 65155AN: 251076Hom.: 9223 AF XY: 0.260 AC XY: 35331AN XY: 135690
GnomAD4 exome AF: 0.301 AC: 439033AN: 1459222Hom.: 68777 Cov.: 42 AF XY: 0.299 AC XY: 216775AN XY: 726054
GnomAD4 genome ? AF: 0.301 AC: 45797AN: 152074Hom.: 7231 Cov.: 32 AF XY: 0.294 AC XY: 21865AN XY: 74338
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 34% of patients studied by a panel of primary immunodeficiencies. Number of patients: 32. Only high quality variants are reported. - |
Immunodeficiency, common variable, 7 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at