chr1-207472818-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000640301.1(CR2):c.67C>T(p.Arg23Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,613,944 control chromosomes in the GnomAD database, including 253 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/10 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. R23L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000640301.1 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.1617C>T | p.Thr539= | synonymous_variant | 10/20 | ENST00000367057.8 | |
CR2 | NM_001877.5 | c.1617C>T | p.Thr539= | synonymous_variant | 10/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CR2 | ENST00000367057.8 | c.1617C>T | p.Thr539= | synonymous_variant | 10/20 | 1 | NM_001006658.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0210 AC: 3190AN: 152134Hom.: 46 Cov.: 32
GnomAD3 exomes AF: 0.0151 AC: 3806AN: 251298Hom.: 38 AF XY: 0.0150 AC XY: 2032AN XY: 135812
GnomAD4 exome AF: 0.0143 AC: 20902AN: 1461692Hom.: 208 Cov.: 31 AF XY: 0.0142 AC XY: 10350AN XY: 727146
GnomAD4 genome AF: 0.0209 AC: 3189AN: 152252Hom.: 45 Cov.: 32 AF XY: 0.0203 AC XY: 1512AN XY: 74458
ClinVar
Submissions by phenotype
Immunodeficiency, common variable, 7 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at