1-207473553-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000367057.8(CR2):c.1987T>C(p.Ser663Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,609,678 control chromosomes in the GnomAD database, including 80,499 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000367057.8 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CR2 | NM_001006658.3 | c.1987T>C | p.Ser663Pro | missense_variant | 11/20 | ENST00000367057.8 | NP_001006659.1 | |
CR2 | NM_001877.5 | c.1979-248T>C | intron_variant | NP_001868.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CR2 | ENST00000367057.8 | c.1987T>C | p.Ser663Pro | missense_variant | 11/20 | 1 | NM_001006658.3 | ENSP00000356024 | P1 |
Frequencies
GnomAD3 genomes AF: 0.334 AC: 50782AN: 151954Hom.: 9317 Cov.: 32
GnomAD3 exomes AF: 0.270 AC: 67724AN: 250936Hom.: 10202 AF XY: 0.269 AC XY: 36476AN XY: 135618
GnomAD4 exome AF: 0.305 AC: 444806AN: 1457606Hom.: 71153 Cov.: 39 AF XY: 0.303 AC XY: 219532AN XY: 725296
GnomAD4 genome AF: 0.334 AC: 50863AN: 152072Hom.: 9346 Cov.: 32 AF XY: 0.327 AC XY: 24289AN XY: 74348
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 35% of patients studied by a panel of primary immunodeficiencies. Number of patients: 33. Only high quality variants are reported. - |
Immunodeficiency, common variable, 7 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at