chr2-134789719-G-A

Variant names:

• chr2-134789719-G-A
• rs1016120
• ENST00000392929.6:n.427-54138C>T

Variant summary

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

The ENST00000392929.6(CCNT2-AS1):​n.427-54138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,050 control chromosomes in the GnomAD database, including 23,477 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 0.51 (23477 hom., cov: 32)
• Consequence: CCNT2-AS1 ENST00000392929.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNT2-AS1	ENST00000392929.6	TSL:4	n.427-54138C>T		intron	N/A
	CCNT2-AS1	ENST00000747809.1		n.166-54138C>T		intron	N/A
	ENSG00000297435	ENST00000747901.1		n.141-1862G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76792 AN: 151932 Hom.: 23438 Cov.: 32

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.506 AC: 76893 AN: 152050 Hom.: 23477 Cov.: 32 AF XY: 0.505 AC XY: 37492 AN XY: 74314

African (AFR) AF: 0.836 AC: 34670 AN: 41474

American (AMR) AF: 0.557 AC: 8513 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2150 AN: 3470

East Asian (EAS) AF: 0.492 AC: 2538 AN: 5162

South Asian (SAS) AF: 0.493 AC: 2376 AN: 4818

European-Finnish (FIN) AF: 0.252 AC: 2660 AN: 10568

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22380 AN: 67960

Other (OTH) AF: 0.553 AC: 1168 AN: 2112

Alfa AF: 0.447 Hom.: 2384

Bravo AF: 0.544

Asia WGS AF: 0.489 AC: 1700 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	0.94
DANN	Benign	0.26
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs1016120; hg19: chr2-135547289;