rs10496732

Variant names:

• chr2-134942049-T-C
• rs10496732
• NM_058241.3:c.431-563T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_058241.3(CCNT2):​c.431-563T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,846 control chromosomes in the GnomAD database, including 3,927 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 0.21 (3927 hom., cov: 31)
• Consequence: CCNT2 NM_058241.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499
• Publications: 11 publications found

Genes affected

CCNT2 (HGNC:1600): (cyclin T2) The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. This cyclin and its kinase partner CDK9 were found to be subunits of the transcription elongation factor p-TEFb. The p-TEFb complex containing this cyclin was reported to interact with, and act as a negative regulator of human immunodeficiency virus type 1 (HIV-1) Tat protein. A pseudogene of this gene is found on chromosome 1. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Dec 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_058241.3. 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
	CCNT2	NM_058241.3	MANE Select	c.431-563T>C		intron	N/A	NP_490595.1	O60583-1
	CCNT2	NM_001241.4		c.431-563T>C		intron	N/A	NP_001232.1	O60583-2
	CCNT2	NM_001320748.2		c.-96-563T>C		intron	N/A	NP_001307677.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNT2	ENST00000264157.10	TSL:1 MANE Select	c.431-563T>C		intron	N/A	ENSP00000264157.5	O60583-1
	CCNT2	ENST00000295238.11	TSL:1	c.431-563T>C		intron	N/A	ENSP00000295238.6	O60583-2
	CCNT2	ENST00000419781.5	TSL:1	n.431-563T>C		intron	N/A	ENSP00000404653.1	F2Z2C9

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32347 AN: 151728 Hom.: 3924 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.213 AC: 32380 AN: 151846 Hom.: 3927 Cov.: 31 AF XY: 0.218 AC XY: 16151 AN XY: 74192

African (AFR) AF: 0.167 AC: 6910 AN: 41408

American (AMR) AF: 0.255 AC: 3891 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3464

East Asian (EAS) AF: 0.0516 AC: 267 AN: 5178

South Asian (SAS) AF: 0.218 AC: 1045 AN: 4804

European-Finnish (FIN) AF: 0.252 AC: 2643 AN: 10508

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15185 AN: 67944

Other (OTH) AF: 0.262 AC: 548 AN: 2094

Alfa AF: 0.230 Hom.: 14189

Bravo AF: 0.207

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		0.50
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10496732; hg19: chr2-135699619;