2-134909561-C-T

Variant names:

• chr2-134909561-C-T
• rs766271
• ENST00000392929.6:n.108+9002G>A

Variant summary

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

The ENST00000392929.6(CCNT2-AS1):​n.108+9002G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,986 control chromosomes in the GnomAD database, including 25,614 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 0.56 (25614 hom., cov: 32)
• Consequence: CCNT2-AS1 ENST00000392929.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 7 publications found

Genes affected

CCNT2-AS1 (HGNC:40130): (CCNT2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000392929.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNT2-AS1	NR_036549.1		n.44+9002G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNT2-AS1	ENST00000392929.6	TSL:4	n.108+9002G>A		intron	N/A
	CCNT2-AS1	ENST00000413962.7	TSL:2	n.177+9002G>A		intron	N/A
	CCNT2-AS1	ENST00000428857.2	TSL:4	n.148+9002G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85766 AN: 151866 Hom.: 25582 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.565 AC: 85855 AN: 151986 Hom.: 25614 Cov.: 32 AF XY: 0.573 AC XY: 42521 AN XY: 74270

African (AFR) AF: 0.685 AC: 28372 AN: 41448

American (AMR) AF: 0.663 AC: 10130 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2827 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3050 AN: 5162

South Asian (SAS) AF: 0.719 AC: 3465 AN: 4818

European-Finnish (FIN) AF: 0.469 AC: 4938 AN: 10534

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31068 AN: 67970

Other (OTH) AF: 0.657 AC: 1387 AN: 2110

Alfa AF: 0.480 Hom.: 4496

Bravo AF: 0.582

Asia WGS AF: 0.669 AC: 2322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.55
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs766271; hg19: chr2-135667131;