chr6-41934770-CATT-C

Variant names:

• chr6-41934770-CATT-C
• rs3218110
• NM_001760.5:c.*1167_*1169delAAT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001760.5(CCND3):​c.*1167_*1169delAAT variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6017 hom., cov: 19)
• Consequence: CCND3 NM_001760.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 6 publications found

Genes affected

CCND3 (HGNC:1585): (cyclin D3) The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. This cyclin forms a complex with and functions as a regulatory subunit of CDK4 or CDK6, whose activtiy is required for cell cycle G1/S transition. This protein has been shown to interact with and be involved in the phosphorylation of tumor suppressor protein Rb. The CDK4 activity associated with this cyclin was reported to be necessary for cell cycle progression through G2 phase into mitosis after UV radiation. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCND3	NM_001760.5	c.*1167_*1169delAAT		downstream_gene_variant		ENST00000372991.9	NP_001751.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCND3	ENST00000372991.9	c.*1167_*1169delAAT		downstream_gene_variant		1	NM_001760.5	ENSP00000362082.5

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41810 AN: 151724 Hom.: 6016 Cov.: 19

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.294

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.275 AC: 41825 AN: 151842 Hom.: 6017 Cov.: 19 AF XY: 0.276 AC XY: 20478 AN XY: 74192

African (AFR) AF: 0.356 AC: 14737 AN: 41368

American (AMR) AF: 0.214 AC: 3270 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3466

East Asian (EAS) AF: 0.174 AC: 904 AN: 5182

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4826

European-Finnish (FIN) AF: 0.272 AC: 2855 AN: 10510

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17068 AN: 67914

Other (OTH) AF: 0.291 AC: 612 AN: 2104

Alfa AF: 0.273 Hom.: 747

Bravo AF: 0.274

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.030

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3218110; hg19: chr6-41902508;