16-30353790-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006110.3(CD2BP2):c.386G>A(p.Arg129Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000212 in 1,602,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006110.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD2BP2 | NM_006110.3 | c.386G>A | p.Arg129Gln | missense_variant | 5/7 | ENST00000305596.8 | NP_006101.1 | |
CD2BP2 | NM_001243646.2 | c.386G>A | p.Arg129Gln | missense_variant | 4/6 | NP_001230575.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD2BP2 | ENST00000305596.8 | c.386G>A | p.Arg129Gln | missense_variant | 5/7 | 1 | NM_006110.3 | ENSP00000304903 | P1 | |
CD2BP2 | ENST00000569466.1 | c.386G>A | p.Arg129Gln | missense_variant | 4/6 | 1 | ENSP00000456935 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000863 AC: 21AN: 243448Hom.: 0 AF XY: 0.0000302 AC XY: 4AN XY: 132564
GnomAD4 exome AF: 0.0000228 AC: 33AN: 1450222Hom.: 0 Cov.: 33 AF XY: 0.00000972 AC XY: 7AN XY: 720338
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.386G>A (p.R129Q) alteration is located in exon 5 (coding exon 4) of the CD2BP2 gene. This alteration results from a G to A substitution at nucleotide position 386, causing the arginine (R) at amino acid position 129 to be replaced by a glutamine (Q). 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