2-134816089-G-C

Variant names:

• chr2-134816089-G-C
• rs749017
• ENST00000392929.6:n.426+51431C>G

Variant summary

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

The ENST00000392929.6(CCNT2-AS1):​n.426+51431C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,124 control chromosomes in the GnomAD database, including 12,518 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 0.39 (12518 hom., cov: 32)
• Consequence: CCNT2-AS1 ENST00000392929.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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.426+51431C>G		intron_variant	Intron 3 of 3	4
CCNT2-AS1	ENST00000668300.1	n.149-4810C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58613 AN: 152006 Hom.: 12513 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.386 AC: 58659 AN: 152124 Hom.: 12518 Cov.: 32 AF XY: 0.386 AC XY: 28710 AN XY: 74384

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.447

Alfa AF: 0.186 Hom.: 357

Bravo AF: 0.405

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs749017; hg19: chr2-135573659;