chr12-4265207-A-G

Variant names:

• chr12-4265207-A-G
• rs11063069
• ENST00000537370.2:n.401+9815T>C

Variant summary

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

The ENST00000537370.2(CCND2-AS1):​n.401+9815T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,200 control chromosomes in the GnomAD database, including 3,017 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 0.19 (3017 hom., cov: 32)
• Consequence: CCND2-AS1 ENST00000537370.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 67 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCND2-AS1	NR_125790.1	n.126+10852T>C		intron_variant	Intron 1 of 1
CCND2-AS1	NR_149145.1	n.182+10089T>C		intron_variant	Intron 1 of 3
CCND2-AS1	NR_149146.1	n.182+10089T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCND2-AS1	ENST00000537370.2	n.401+9815T>C		intron_variant	Intron 1 of 2	4
CCND2-AS1	ENST00000539135.1	n.126+10852T>C		intron_variant	Intron 1 of 1	3
CCND2-AS1	ENST00000646138.1	n.182+10089T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29481 AN: 152082 Hom.: 3015 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0446

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.194 AC: 29493 AN: 152200 Hom.: 3017 Cov.: 32 AF XY: 0.190 AC XY: 14131 AN XY: 74412

African (AFR) AF: 0.195 AC: 8077 AN: 41512

American (AMR) AF: 0.148 AC: 2259 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3470

East Asian (EAS) AF: 0.0445 AC: 231 AN: 5186

South Asian (SAS) AF: 0.143 AC: 690 AN: 4826

European-Finnish (FIN) AF: 0.231 AC: 2442 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14398 AN: 68012

Other (OTH) AF: 0.197 AC: 417 AN: 2112

Alfa AF: 0.201 Hom.: 13646

Bravo AF: 0.187

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs11063069; hg19: chr12-4374373;