rs6710823

Positions:

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNT2-AS1	ENST00000392929.6	n.426+32709C>T		intron_variant, non_coding_transcript_variant		4
CCNT2-AS1	ENST00000668300.1	n.149-23532C>T		intron_variant, non_coding_transcript_variant

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;