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GeneBe

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

2
Splicing: ADA: 0.4188
2

Clinical Significance

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

Conservation

PhyloP100: 5.13

Links

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
CCND1NM_053056.3 linkuse as main transcriptc.723G>A p.Pro241= splice_region_variant, synonymous_variant 4/5 ENST00000227507.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCND1ENST00000227507.3 linkuse as main transcriptc.723G>A p.Pro241= splice_region_variant, synonymous_variant 4/51 NM_053056.3 P1
CCND1ENST00000542367.1 linkuse as main transcriptn.186G>A splice_region_variant, non_coding_transcript_exon_variant 1/21
CCND1ENST00000536559.1 linkuse as main transcriptc.*143G>A 3_prime_UTR_variant 2/23
CCND1ENST00000545484.1 linkuse as main transcriptn.429G>A non_coding_transcript_exon_variant 2/25

Frequencies

GnomAD3 genomes
AF:
0.393
AC:
59681
AN:
152010
Hom.:
12647
Cov.:
33
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 submitterclinical testingGeneDxApr 16, 2020This 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 providedliterature onlyOMIMMay 01, 2013- -
Colorectal cancer, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMMay 01, 2013- -
VON HIPPEL-LINDAU SYNDROME, MODIFIER OF Other:1
risk factor, no assertion criteria providedliterature onlyOMIMMay 01, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.44
Cadd
Benign
22
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.

Other links and lift over

dbSNP: rs9344; hg19: chr11-69462910; COSMIC: COSV57118864; COSMIC: COSV57118864;