12-4263966-A-G

Variant names:

• chr12-4263966-A-G
• rs4631962
• ENST00000537370.2:n.402-10781T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000539135.1(CCND2-AS1):​n.126+12093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,976 control chromosomes in the GnomAD database, including 22,293 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 0.52 (22293 hom., cov: 31)
• Consequence: CCND2-AS1 ENST00000539135.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 8 publications found

Genes affected

CCND2-AS1 (HGNC:49398): (CCND2 antisense RNA 1)

ENSG00000298091 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539135.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCND2-AS1	NR_125790.1		n.126+12093T>C		intron	N/A
	CCND2-AS1	NR_149145.1		n.183-10781T>C		intron	N/A
	CCND2-AS1	NR_149146.1		n.182+11330T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCND2-AS1	ENST00000537370.2	TSL:4	n.402-10781T>C		intron	N/A
	CCND2-AS1	ENST00000539135.1	TSL:3	n.126+12093T>C		intron	N/A
	CCND2-AS1	ENST00000646138.1		n.183-9763T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78580 AN: 151860 Hom.: 22283 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.517 AC: 78618 AN: 151976 Hom.: 22293 Cov.: 31 AF XY: 0.520 AC XY: 38612 AN XY: 74268

African (AFR) AF: 0.272 AC: 11262 AN: 41474

American (AMR) AF: 0.590 AC: 9001 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2069 AN: 3468

East Asian (EAS) AF: 0.700 AC: 3617 AN: 5164

South Asian (SAS) AF: 0.670 AC: 3222 AN: 4812

European-Finnish (FIN) AF: 0.508 AC: 5354 AN: 10546

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42318 AN: 67936

Other (OTH) AF: 0.546 AC: 1154 AN: 2112

Alfa AF: 0.589 Hom.: 19995

Bravo AF: 0.511

Asia WGS AF: 0.663 AC: 2306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		-0.0050

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4631962;

hg19: chr12-4373132;