1-207454348-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001006658.3(CR2):c.-71T>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,339,174 control chromosomes in the GnomAD database, including 25,992 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001006658.3 5_prime_UTR_premature_start_codon_gain
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CR2 | NM_001006658.3 | c.-71T>C | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 20 | ENST00000367057.8 | NP_001006659.1 | ||
CR2 | NM_001006658.3 | c.-71T>C | 5_prime_UTR_variant | Exon 1 of 20 | ENST00000367057.8 | NP_001006659.1 | ||
CR2 | NM_001877.5 | c.-71T>C | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 19 | NP_001868.2 | |||
CR2 | NM_001877.5 | c.-71T>C | 5_prime_UTR_variant | Exon 1 of 19 | NP_001868.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CR2 | ENST00000367057 | c.-71T>C | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 20 | 1 | NM_001006658.3 | ENSP00000356024.3 | |||
CR2 | ENST00000367057 | c.-71T>C | 5_prime_UTR_variant | Exon 1 of 20 | 1 | NM_001006658.3 | ENSP00000356024.3 |
Frequencies
GnomAD3 genomes AF: 0.158 AC: 24052AN: 152074Hom.: 2032 Cov.: 32
GnomAD4 exome AF: 0.196 AC: 232140AN: 1186982Hom.: 23960 Cov.: 17 AF XY: 0.196 AC XY: 116461AN XY: 595314
GnomAD4 genome AF: 0.158 AC: 24057AN: 152192Hom.: 2032 Cov.: 32 AF XY: 0.155 AC XY: 11552AN XY: 74430
ClinVar
Submissions by phenotype
Immunodeficiency, common variable, 7 Benign:2
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not provided Benign:2
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This variant is associated with the following publications: (PMID: 22673213, 23612877, 17360460) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at