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. The variant received -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
• Publications: 23 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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.426+32709C>T		intron	N/A
	CCNT2-AS1	ENST00000668300.1		n.149-23532C>T		intron	N/A
	CCNT2-AS1	ENST00000747809.1		n.165+42709C>T		intron	N/A

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

African (AFR) AF: 0.321 AC: 807 AN: 2514

American (AMR) AF: 0.172 AC: 234 AN: 1358

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 125 AN: 424

East Asian (EAS) AF: 0.255 AC: 99 AN: 388

South Asian (SAS) AF: 0.146 AC: 30 AN: 206

European-Finnish (FIN) AF: 0.115 AC: 77 AN: 668

Middle Eastern (MID) AF: 0.292 AC: 7 AN: 24

European-Non Finnish (NFE) AF: 0.216 AC: 1481 AN: 6854

Other (OTH) AF: 0.300 AC: 57 AN: 190

Alfa AF: 0.470 Hom.: 12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.27
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6710823;

hg19: chr2-135592381;