chr2-134797922-T-C

Variant names:

• chr2-134797922-T-C
• rs1942043
• ENST00000392929.6:n.427-62341A>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.427-62341A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,278 control chromosomes in the GnomAD database, including 292 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 (292 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCNT2-AS1 ENST00000392929.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 publications found

Genes affected

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

VDAC2P4 (HGNC:51932): (VDAC2 pseudogene 4)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 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.427-62341A>G		intron	N/A
	CCNT2-AS1	ENST00000747809.1		n.166-62341A>G		intron	N/A
	VDAC2P4	ENST00000452925.1	TSL:6	n.*43T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7449 AN: 152160 Hom.: 288 Cov.: 32

Gnomad AFR AF: 0.0655

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0615

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0516

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0491 AC: 7478 AN: 152278 Hom.: 292 Cov.: 32 AF XY: 0.0508 AC XY: 3780 AN XY: 74478

African (AFR) AF: 0.0658 AC: 2734 AN: 41562

American (AMR) AF: 0.116 AC: 1774 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0615 AC: 213 AN: 3464

East Asian (EAS) AF: 0.113 AC: 583 AN: 5178

South Asian (SAS) AF: 0.0481 AC: 232 AN: 4828

European-Finnish (FIN) AF: 0.0374 AC: 397 AN: 10620

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0207 AC: 1411 AN: 68016

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0321 Hom.: 35

Bravo AF: 0.0569

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.41
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs1942043; hg19: chr2-135555492;