rs803054

Variant names:

• chr5-132750285-A-G
• rs803054
• NM_001039780.4:c.634-572A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-132750285-A-G
• chr5-132750285-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

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 = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039780.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNI2	NM_001039780.4	MANE Select	c.634-572A>G		intron	N/A	NP_001034869.1
	CCNI2	NM_001287252.2		c.634-572A>G		intron	N/A	NP_001274181.1
	CCNI2	NM_001287253.2		c.637-572A>G		intron	N/A	NP_001274182.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNI2	ENST00000378731.6	TSL:1 MANE Select	c.634-572A>G		intron	N/A	ENSP00000368005.1
	CCNI2	ENST00000614847.1	TSL:1	c.634-572A>G		intron	N/A	ENSP00000478257.1
	CCNI2	ENST00000492179.1	TSL:3	n.54-572A>G		intron	N/A

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

African (AFR) AF: 0.450 AC: 18657 AN: 41432

American (AMR) AF: 0.228 AC: 3486 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3468

East Asian (EAS) AF: 0.729 AC: 3775 AN: 5178

South Asian (SAS) AF: 0.156 AC: 751 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2306 AN: 10586

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0943 AC: 6415 AN: 67994

Other (OTH) AF: 0.203 AC: 428 AN: 2106

Alfa AF: 0.124 Hom.: 3738

Bravo AF: 0.256

Asia WGS AF: 0.407 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.67
PhyloP100		-0.0060
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: rs803054; hg19: chr5-132085977;