6-41946640-A-G

Position:

• chr6-41946640-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136017.3(CCND3):​c.-45-6055T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 146,576 control chromosomes in the GnomAD database, including 4,192 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4192 hom., cov: 26)
• Consequence: CCND3 NM_001136017.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760

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]

CCND3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCND3	NM_001136017.3	c.-45-6055T>C		intron_variant			NP_001129489.1
CCND3	NM_001424053.1	c.-45-6055T>C		intron_variant			NP_001410982.1
CCND3	NM_001424055.1	c.-45-6055T>C		intron_variant			NP_001410984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCND3	ENST00000372988.8	c.-45-6055T>C		intron_variant		1		ENSP00000362079.4
CCND3	ENST00000511642.5	c.-45-6055T>C		intron_variant		2		ENSP00000426212.1
CCND3	ENST00000510503.5	c.-45-6055T>C		intron_variant		3		ENSP00000425986.1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 33473 AN: 146490 Hom.: 4188 Cov.: 26

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.228 AC: 33484 AN: 146576 Hom.: 4192 Cov.: 26 AF XY: 0.224 AC XY: 15896 AN XY: 70940

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.214

Alfa AF: 0.255 Hom.: 4941

Bravo AF: 0.226

Asia WGS AF: 0.223 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9349204; hg19: chr6-41914378;