11-69648710-AGG-AG

Position:

• chr11-69648710-AGG-AG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_053056.3(CCND1):​c.723+571del variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (17190 hom., cov: 0)
• Consequence: CCND1 NM_053056.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.78

Genes affected

CCND1 (HGNC:1582): (cyclin D1) The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance throughout 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 activity is required for cell cycle G1/S transition. This protein has been shown to interact with tumor suppressor protein Rb and the expression of this gene is regulated positively by Rb. Mutations, amplification and overexpression of this gene, which alters cell cycle progression, are observed frequently in a variety of human cancers. [provided by RefSeq, Dec 2019]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCND1	NM_053056.3	c.723+571del		intron_variant		ENST00000227507.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCND1	ENST00000227507.3	c.723+571del		intron_variant		1	NM_053056.3	P1
CCND1	ENST00000542367.1	n.186+571del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68151 AN: 152018 Hom.: 17198 Cov.: 0

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.448 AC: 68148 AN: 152134 Hom.: 17190 Cov.: 0 AF XY: 0.455 AC XY: 33821 AN XY: 74366

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.472

Alfa AF: 0.476 Hom.: 2250

Bravo AF: 0.428

Asia WGS AF: 0.622 AC: 2159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3212879; hg19: chr11-69463478;