rs13088006

chr3-133576341-T-C

Variant summary

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

The NM_017548.5(CDV3):c.317+1226T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,910 control chromosomes in the GnomAD database, including 13,570 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 0.36 (13570 hom., cov: 33)
• Consequence: CDV3 NM_017548.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

CDV3 (HGNC:26928): (CDV3 homolog) Located in cytosol and plasma membrane. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDV3	NM_017548.5	c.317+1226T>C		intron_variant		ENST00000264993.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDV3	ENST00000264993.8	c.317+1226T>C		intron_variant		1	NM_017548.5	P3

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54799 AN: 151790 Hom.: 13529 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.361 AC: 54891 AN: 151910 Hom.: 13570 Cov.: 33 AF XY: 0.363 AC XY: 26918 AN XY: 74236

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.324

Alfa AF: 0.289 Hom.: 1142

Bravo AF: 0.380

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.6
Dann	Benign	0.63

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: rs13088006; hg19: chr3-133295185;