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
NM_053056 splice_region, synonymous
Scores
2
Splicing: ADA: 0.4188
2
Clinical Significance
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 |
---|---|---|---|---|---|---|---|
CCND1 | NM_053056.3 | 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 | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCND1 | ENST00000227507.3 | c.723G>A | p.Pro241= | splice_region_variant, synonymous_variant | 4/5 | 1 | NM_053056.3 | P1 | |
CCND1 | ENST00000542367.1 | n.186G>A | splice_region_variant, non_coding_transcript_exon_variant | 1/2 | 1 | ||||
CCND1 | ENST00000536559.1 | c.*143G>A | 3_prime_UTR_variant | 2/2 | 3 | ||||
CCND1 | ENST00000545484.1 | n.429G>A | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.393 AC: 59681AN: 152010Hom.: 12647 Cov.: 33
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GnomAD3 exomes AF: 0.453 AC: 113515AN: 250702Hom.: 26634 AF XY: 0.464 AC XY: 62937AN XY: 135576
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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:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
Find out detailed SpliceAI scores and Pangolin per-transcript scores at