rs4672907

chr2-218956447-G-A

Variant summary

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

The ENST00000429343.1(CDK5R2-AS1):n.45+5412C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK5R2-AS1	ENST00000429343.1	n.45+5412C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.268

Alfa AF: 0.214 Hom.: 2399

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4672907; hg19: chr2-219821169;