rs1016120

Positions:

• chr2-134789719-G-A
• chr2-134789719-G-C
• chr2-134789719-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392929.6(CCNT2-AS1):​n.427-54138C>T 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 0.506 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNT2-AS1	ENST00000392929.6	n.427-54138C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.553

Alfa AF: 0.431 Hom.: 2111

Bravo AF: 0.544

Asia WGS AF: 0.489 AC: 1700 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	0.94
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1016120; hg19: chr2-135547289;