rs2597167

chr17-47970290-T-C

Variant summary

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

The ENST00000579632.5(CDK5RAP3):c.-30-323T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,224 control chromosomes in the GnomAD database, including 66,897 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 0.94 (66897 hom., cov: 32)
• Consequence: CDK5RAP3 ENST00000579632.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

Genes affected

CDK5RAP3 (HGNC:18673): (CDK5 regulatory subunit associated protein 3) This gene encodes a protein that has been reported to function in signaling pathways governing transcriptional regulation and cell cycle progression. It may play a role in tumorigenesis and metastasis. A pseudogene of this gene is located on the long arm of chromosome 20. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK5RAP3	XM_011525297.1	c.-30-323T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK5RAP3	ENST00000579632.5	c.-30-323T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142295 AN: 152106 Hom.: 66856 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.966

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.935 AC: 142392 AN: 152224 Hom.: 66897 Cov.: 32 AF XY: 0.935 AC XY: 69604 AN XY: 74432

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.969

Gnomad4 ASJ AF: 0.966

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.980

Gnomad4 OTH AF: 0.953

Alfa AF: 0.972 Hom.: 77388

Bravo AF: 0.932

Asia WGS AF: 0.956 AC: 3324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.0
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2597167; hg19: chr17-46047656;