chr2-134816089-G-C

Position:

• chr2-134816089-G-C

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNT2-AS1	ENST00000392929.6	n.426+51431C>G		intron_variant, non_coding_transcript_variant		4
CCNT2-AS1	ENST00000668300.1	n.149-4810C>G		intron_variant, non_coding_transcript_variant

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;