1-116764484-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001767.5(CD2):āc.614A>Gā(p.Glu205Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001767.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD2 | NM_001767.5 | c.614A>G | p.Glu205Gly | missense_variant, splice_region_variant | 4/5 | ENST00000369478.4 | |
CD2 | NM_001328609.2 | c.692A>G | p.Glu231Gly | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD2 | ENST00000369478.4 | c.614A>G | p.Glu205Gly | missense_variant, splice_region_variant | 4/5 | 1 | NM_001767.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152098Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251044Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135700
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461570Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 727108
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152098Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2024 | The c.614A>G (p.E205G) alteration is located in exon 4 (coding exon 4) of the CD2 gene. This alteration results from a A to G substitution at nucleotide position 614, causing the glutamic acid (E) at amino acid position 205 to be replaced by a glycine (G). 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