rs9344

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The NM_053056(CCND1):c.723G>A(p.Pro241=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.393 in 152010 control chromosomes in the gnomAD Genomes database, including 12647 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.39 ( 12647 hom., cov: 33)

Exomes 𝑓: 0.45 ( 26634 hom. )

Consequence

CCND1
NM_053056 splice_region, synonymous

Scores

Splicing: ADA: 0.4188

Clinical Significance

Benign criteria provided, single submitter B:1O:3

Conservation

PhyloP100: 5.13

Links

CCND1 (HGNC:1582):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 11:69648142-G>A is Benign according to our data. Variant chr11-69648142-G-A is described in ClinVar as [Benign]. Clinvar id is 13755. Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-69648142-G-A is described in Lovd as [Benign].

BA1

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCND1	NM_053056.3 linkuse as main transcript	c.723G>A	p.Pro241=	splice_region_variant, synonymous_variant	4/5	ENST00000227507.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
CCND1	ENST00000227507.3 linkuse as main transcript	c.723G>A	p.Pro241=	splice_region_variant, synonymous_variant	4/5	1	NM_053056.3	P1
CCND1	ENST00000542367.1 linkuse as main transcript	n.186G>A		splice_region_variant, non_coding_transcript_exon_variant	1/2	1
CCND1	ENST00000536559.1 linkuse as main transcript	c.*143G>A		3_prime_UTR_variant	2/2	3
CCND1	ENST00000545484.1 linkuse as main transcript	n.429G>A		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59681

AN:

152010

Hom.:

12647

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.395

Gnomad AMR

AF:

0.404

Gnomad ASJ

AF:

0.446

Gnomad EAS

AF:

0.549

Gnomad SAS

AF:

0.523

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.429

GnomAD3 exomes

AF:

0.453

AC:

113515

AN:

250702

Hom.:

26634

AF XY:

0.464

AC XY:

62937

AN XY:

135576

show subpopulations

Gnomad AFR exome

AF:

0.215

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.448

Gnomad EAS exome

AF:

0.569

Gnomad SAS exome

AF:

0.522

Gnomad FIN exome

AF:

0.486

Gnomad NFE exome

AF:

0.466

Gnomad OTH exome

AF:

0.462

GnomAD4 exome

AF:

0.449

AC:

656603

AN:

1461040

Hom.:

149575

AF XY:

0.454

AC XY:

329998

AN XY:

726820

show subpopulations

Gnomad4 AFR exome

AF:

0.215

Gnomad4 AMR exome

AF:

0.379

Gnomad4 ASJ exome

AF:

0.444

Gnomad4 EAS exome

AF:

0.523

Gnomad4 SAS exome

AF:

0.523

Gnomad4 FIN exome

AF:

0.481

Gnomad4 NFE exome

AF:

0.449

Gnomad4 OTH exome

AF:

0.455

Alfa

AF:

0.449

Hom.:

21060

Bravo

AF:

0.380

Asia WGS

AF:

0.508

AC:

1766

AN:

3478

EpiCase

AF:

0.470

EpiControl

AF:

0.469

ClinVar

Significance: Benign

Submissions summary: Benign:1Other:3

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 16, 2020

This variant is associated with the following publications: (PMID: 26617896, 25997217, 16783567, 21268129, 11896626, 7675441, 10667569, 20680537, 22606291, 23502783, 21594903, 21161398, 24270739, 21107342, 17308274, 17960397, 11418364, 22304571, 20380574, 18843022, 22901215, 21273603) -

MULTIPLE MYELOMA, t(11;14) TYPE, SUSCEPTIBILITY TO

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

May 01, 2013

- -

Colorectal cancer, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

May 01, 2013

- -

VON HIPPEL-LINDAU SYNDROME, MODIFIER OF

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

May 01, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

Cadd

Benign

Dann

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.42

dbscSNV1_RF

Benign

0.39

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over