rs6691117
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000651.6(CR1):āc.6193A>Gā(p.Ile2065Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,612,446 control chromosomes in the GnomAD database, including 69,496 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_000651.6 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 |
---|---|---|---|---|---|---|---|---|
CR1 | NM_000651.6 | c.6193A>G | p.Ile2065Val | missense_variant | 37/47 | ENST00000367049.9 | NP_000642.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CR1 | ENST00000367049.9 | c.6193A>G | p.Ile2065Val | missense_variant | 37/47 | 5 | NM_000651.6 | ENSP00000356016.4 |
Frequencies
GnomAD3 genomes AF: 0.400 AC: 60820AN: 151966Hom.: 16765 Cov.: 31
GnomAD3 exomes AF: 0.321 AC: 79225AN: 246530Hom.: 15674 AF XY: 0.315 AC XY: 42110AN XY: 133756
GnomAD4 exome AF: 0.243 AC: 355524AN: 1460362Hom.: 52693 Cov.: 37 AF XY: 0.248 AC XY: 179804AN XY: 726362
GnomAD4 genome AF: 0.401 AC: 60914AN: 152084Hom.: 16803 Cov.: 31 AF XY: 0.402 AC XY: 29871AN XY: 74350
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2021 | This variant is associated with the following publications: (PMID: 23856853, 31182772, 21700265, 24018213, 23591632) - |
CR1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at