rs16831005

Variant names:

• chr2-134779762-T-C
• rs16831005
• ENST00000392929.6:n.427-44181A>G

Variant summary

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

The ENST00000392929.6(CCNT2-AS1):​n.427-44181A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 152,248 control chromosomes in the GnomAD database, including 483 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 0.049 (483 hom., cov: 32)
• Consequence: CCNT2-AS1 ENST00000392929.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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.427-44181A>G		intron_variant	Intron 3 of 3	4
CCNT2-AS1	ENST00000747809.1	n.166-44181A>G		intron_variant	Intron 2 of 3
ENSG00000297435	ENST00000747901.1	n.140+6082T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7454 AN: 152130 Hom.: 485 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00351

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0490 AC: 7463 AN: 152248 Hom.: 483 Cov.: 32 AF XY: 0.0518 AC XY: 3855 AN XY: 74446

African (AFR) AF: 0.105 AC: 4353 AN: 41536

American (AMR) AF: 0.0712 AC: 1089 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1341 AN: 5174

South Asian (SAS) AF: 0.0441 AC: 213 AN: 4828

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10624

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00351 AC: 239 AN: 68008

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0273 Hom.: 65

Bravo AF: 0.0579

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.22
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs16831005; hg19: chr2-135537332;