rs6710823

Variant names:

• chr2-134834811-G-A
• rs6710823
• ENST00000392929.6:n.426+32709C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-134834811-G-A
• chr2-134834811-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+32709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.23 (170 hom., cov: 1)
• Consequence: CCNT2-AS1 ENST00000392929.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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 = 0.303 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+32709C>T		intron_variant	Intron 3 of 3	4
CCNT2-AS1	ENST00000668300.1	n.149-23532C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.231 AC: 2938 AN: 12706 Hom.: 170 Cov.: 1

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.231 AC: 2942 AN: 12716 Hom.: 170 Cov.: 1 AF XY: 0.228 AC XY: 1322 AN XY: 5802

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.300

Alfa AF: 0.470 Hom.: 12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6710823; hg19: chr2-135592381;