rs803054

chr5-132750285-A-Gchr5-132750285-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039780.4(CCNI2):c.634-572A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,066 control chromosomes in the GnomAD database, including 6,737 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 0.24 (6737 hom., cov: 32)
• Consequence: CCNI2 NM_001039780.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

CCNI2 (HGNC:33869): (cyclin I family member 2) Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be involved in mitotic cell cycle phase transition and regulation of cyclin-dependent protein serine/threonine kinase activity. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -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 = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCNI2	NM_001039780.4	c.634-572A>G		intron_variant		ENST00000378731.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNI2	ENST00000378731.6	c.634-572A>G		intron_variant		1	NM_001039780.4	A2
CCNI2	ENST00000614847.1	c.634-572A>G		intron_variant		1		P2
CCNI2	ENST00000492179.1	n.54-572A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36215 AN: 151948 Hom.: 6722 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.239 AC: 36296 AN: 152066 Hom.: 6737 Cov.: 32 AF XY: 0.245 AC XY: 18192 AN XY: 74342

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.203

Alfa AF: 0.111 Hom.: 2016

Bravo AF: 0.256

Asia WGS AF: 0.407 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.6
Dann	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs803054; hg19: chr5-132085977;