2-134782397-C-T

Variant names:

• chr2-134782397-C-T
• rs6430538
• ENST00000392929.6:n.427-46816G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392929.6(CCNT2-AS1):​n.427-46816G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,100 control chromosomes in the GnomAD database, including 33,352 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 0.62 (33352 hom., cov: 32)
• Consequence: CCNT2-AS1 ENST00000392929.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNT2-AS1	ENST00000392929.6	n.427-46816G>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94332 AN: 151982 Hom.: 33285 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.621 AC: 94465 AN: 152100 Hom.: 33352 Cov.: 32 AF XY: 0.626 AC XY: 46575 AN XY: 74358

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.687

Alfa AF: 0.516 Hom.: 27813

Bravo AF: 0.660

Asia WGS AF: 0.884 AC: 3072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6430538; hg19: chr2-135539967;