chr1-116768613-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001767.5(CD2):c.886C>T(p.Arg296Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000096 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001767.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD2 | NM_001767.5 | c.886C>T | p.Arg296Cys | missense_variant | 5/5 | ENST00000369478.4 | |
CD2 | NM_001328609.2 | c.964C>T | p.Arg322Cys | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD2 | ENST00000369478.4 | c.886C>T | p.Arg296Cys | missense_variant | 5/5 | 1 | NM_001767.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000132 AC: 20AN: 152086Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251378Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135892
GnomAD4 exome AF: 0.0000923 AC: 135AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.000106 AC XY: 77AN XY: 727246
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152204Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.886C>T (p.R296C) alteration is located in exon 5 (coding exon 5) of the CD2 gene. This alteration results from a C to T substitution at nucleotide position 886, causing the arginine (R) at amino acid position 296 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at