chr1-207526788-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_000651.6(CR1):c.922C>T(p.Arg308Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000215 in 1,517,564 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000651.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CR1 | NM_000651.6 | c.922C>T | p.Arg308Cys | missense_variant | 6/47 | ENST00000367049.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CR1 | ENST00000367049.9 | c.922C>T | p.Arg308Cys | missense_variant | 6/47 | 5 | NM_000651.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000953 AC: 12AN: 125890Hom.: 1 Cov.: 21
GnomAD3 exomes AF: 0.000153 AC: 34AN: 221586Hom.: 2 AF XY: 0.000141 AC XY: 17AN XY: 120600
GnomAD4 exome AF: 0.000226 AC: 314AN: 1391674Hom.: 39 Cov.: 31 AF XY: 0.000217 AC XY: 150AN XY: 691370
GnomAD4 genome ? AF: 0.0000953 AC: 12AN: 125890Hom.: 1 Cov.: 21 AF XY: 0.0000656 AC XY: 4AN XY: 60978
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2022 | The c.922C>T (p.R308C) alteration is located in exon 6 (coding exon 6) of the CR1 gene. This alteration results from a C to T substitution at nucleotide position 922, causing the arginine (R) at amino acid position 308 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | CR1: PP2, BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at