rs4672907

Variant names:

• chr2-218956447-G-A
• rs4672907
• ENST00000429343.1:n.45+5412C>T

Variant summary

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

The ENST00000429343.1(CDK5R2-AS1):​n.45+5412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,018 control chromosomes in the GnomAD database, including 8,206 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 0.29 (8206 hom., cov: 32)
• Consequence: CDK5R2-AS1 ENST00000429343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 9 publications found

Genes affected

CDK5R2-AS1 (HGNC:55677): (CDK5R2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK5R2-AS1	ENST00000429343.1	n.45+5412C>T		intron_variant	Intron 1 of 1	4
CDK5R2-AS1	ENST00000715606.1	n.282+2738C>T		intron_variant	Intron 1 of 4
CDK5R2-AS1	ENST00000715607.2	n.650+2244C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43532 AN: 151900 Hom.: 8182 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.287 AC: 43603 AN: 152018 Hom.: 8206 Cov.: 32 AF XY: 0.284 AC XY: 21087 AN XY: 74282

African (AFR) AF: 0.535 AC: 22166 AN: 41418

American (AMR) AF: 0.256 AC: 3903 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3464

East Asian (EAS) AF: 0.326 AC: 1680 AN: 5160

South Asian (SAS) AF: 0.261 AC: 1257 AN: 4820

European-Finnish (FIN) AF: 0.157 AC: 1660 AN: 10582

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11665 AN: 67988

Other (OTH) AF: 0.268 AC: 566 AN: 2110

Alfa AF: 0.213 Hom.: 3214

Bravo AF: 0.307

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.49
DANN	Benign	0.57
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs4672907; hg19: chr2-219821169;