ENST00000537370.2:n.402-6001A>G

Variant names:

• chr12-4259186-T-C
• rs10774214
• ENST00000537370.2:n.402-6001A>G

Variant summary

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

The ENST00000537370.2(CCND2-AS1):​n.402-6001A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,996 control chromosomes in the GnomAD database, including 23,480 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 0.54 (23480 hom., cov: 32)
• Consequence: CCND2-AS1 ENST00000537370.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 57 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCND2-AS1	NR_125790.1	n.127-9993A>G		intron_variant	Intron 1 of 1
CCND2-AS1	NR_149145.1	n.183-6001A>G		intron_variant	Intron 1 of 3
CCND2-AS1	NR_149146.1	n.183-9993A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCND2-AS1	ENST00000537370.2	n.402-6001A>G		intron_variant	Intron 1 of 2	4
CCND2-AS1	ENST00000539135.1	n.127-9993A>G		intron_variant	Intron 1 of 1	3
CCND2-AS1	ENST00000646138.1	n.183-4983A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82466 AN: 151878 Hom.: 23468 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.543 AC: 82522 AN: 151996 Hom.: 23480 Cov.: 32 AF XY: 0.543 AC XY: 40373 AN XY: 74292

African (AFR) AF: 0.368 AC: 15280 AN: 41466

American (AMR) AF: 0.575 AC: 8781 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2074 AN: 3472

East Asian (EAS) AF: 0.670 AC: 3465 AN: 5174

South Asian (SAS) AF: 0.676 AC: 3261 AN: 4822

European-Finnish (FIN) AF: 0.509 AC: 5359 AN: 10522

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.625 AC: 42501 AN: 67964

Other (OTH) AF: 0.563 AC: 1184 AN: 2102

Alfa AF: 0.592 Hom.: 56559

Bravo AF: 0.537

Asia WGS AF: 0.662 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.85
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10774214; hg19: chr12-4368352;