rs142170178
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001759.4(CCND2):c.785G>A(p.Arg262His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00068 in 1,614,118 control chromosomes in the GnomAD database, including 6 homozygotes. 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 Likely benign (★★).
Frequency
Consequence
NM_001759.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCND2 | NM_001759.4 | c.785G>A | p.Arg262His | missense_variant | 5/5 | ENST00000261254.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCND2 | ENST00000261254.8 | c.785G>A | p.Arg262His | missense_variant | 5/5 | 1 | NM_001759.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00110 AC: 168AN: 152150Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00112 AC: 282AN: 251364Hom.: 2 AF XY: 0.00108 AC XY: 147AN XY: 135850
GnomAD4 exome AF: 0.000635 AC: 929AN: 1461850Hom.: 5 Cov.: 31 AF XY: 0.000593 AC XY: 431AN XY: 727232
GnomAD4 genome ? AF: 0.00110 AC: 168AN: 152268Hom.: 1 Cov.: 32 AF XY: 0.00130 AC XY: 97AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | CCND2: BP4, BS1, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Dec 30, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 23, 2021 | This variant is associated with the following publications: (PMID: 29642553) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at