chr2-134932491-C-T

Variant names:

• chr2-134932491-C-T
• rs12470730
• NM_058241.3:c.241-4350C>T

Variant summary

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

The NM_058241.3(CCNT2):​c.241-4350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,018 control chromosomes in the GnomAD database, including 4,285 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 0.23 (4285 hom., cov: 32)
• Consequence: CCNT2 NM_058241.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCNT2	NM_058241.3	c.241-4350C>T		intron_variant	Intron 2 of 8	ENST00000264157.10	NP_490595.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNT2	ENST00000264157.10	c.241-4350C>T		intron_variant	Intron 2 of 8	1	NM_058241.3	ENSP00000264157.5

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35078 AN: 151896 Hom.: 4283 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.231 AC: 35105 AN: 152018 Hom.: 4285 Cov.: 32 AF XY: 0.232 AC XY: 17243 AN XY: 74326

African (AFR) AF: 0.233 AC: 9673 AN: 41448

American (AMR) AF: 0.285 AC: 4355 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1101 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2068 AN: 5172

South Asian (SAS) AF: 0.374 AC: 1798 AN: 4812

European-Finnish (FIN) AF: 0.165 AC: 1743 AN: 10554

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13598 AN: 67980

Other (OTH) AF: 0.282 AC: 594 AN: 2104

Alfa AF: 0.218 Hom.: 1968

Bravo AF: 0.241

Asia WGS AF: 0.371 AC: 1291 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		-0.29
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: rs12470730; hg19: chr2-135690061;