2-134782397-C-T

Position:

• chr2-134782397-C-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNT2-AS1	ENST00000392929.6	n.427-46816G>A		intron_variant, non_coding_transcript_variant		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;