2-134782397-C-T

Variant names:

• chr2-134782397-C-T
• rs6430538
• ENST00000392929.6:n.427-46816G>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.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
• Publications: 63 publications found

Genes affected

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

ENSG00000297435 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNT2-AS1	ENST00000392929.6	TSL:4	n.427-46816G>A		intron	N/A
	CCNT2-AS1	ENST00000747809.1		n.166-46816G>A		intron	N/A
	ENSG00000297435	ENST00000747901.1		n.140+8717C>T		intron	N/A

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

African (AFR) AF: 0.897 AC: 37228 AN: 41512

American (AMR) AF: 0.713 AC: 10892 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2550 AN: 3470

East Asian (EAS) AF: 0.979 AC: 5061 AN: 5172

South Asian (SAS) AF: 0.780 AC: 3765 AN: 4824

European-Finnish (FIN) AF: 0.367 AC: 3878 AN: 10578

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29070 AN: 67948

Other (OTH) AF: 0.687 AC: 1447 AN: 2106

Alfa AF: 0.512 Hom.: 68195

Bravo AF: 0.660

Asia WGS AF: 0.884 AC: 3072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		-0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6430538;

hg19: chr2-135539967;