3-133576341-T-C

Variant names:

• chr3-133576341-T-C
• rs13088006
• NM_017548.5:c.317+1226T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017548.5. 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
	CDV3	NM_017548.5	MANE Select	c.317+1226T>C		intron	N/A	NP_060018.1
	CDV3	NM_001410823.1		c.317+1226T>C		intron	N/A	NP_001397752.1
	CDV3	NM_001134422.2		c.317+1226T>C		intron	N/A	NP_001127894.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDV3	ENST00000264993.8	TSL:1 MANE Select	c.317+1226T>C		intron	N/A	ENSP00000264993.3
	CDV3	ENST00000431519.6	TSL:1	c.317+1226T>C		intron	N/A	ENSP00000391955.2
	CDV3	ENST00000688838.1		c.317+1226T>C		intron	N/A	ENSP00000508628.1

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

African (AFR) AF: 0.704 AC: 29091 AN: 41332

American (AMR) AF: 0.314 AC: 4795 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1685 AN: 5176

South Asian (SAS) AF: 0.359 AC: 1732 AN: 4826

European-Finnish (FIN) AF: 0.273 AC: 2878 AN: 10550

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12872 AN: 67968

Other (OTH) AF: 0.324 AC: 682 AN: 2108

Alfa AF: 0.304 Hom.: 1320

Bravo AF: 0.380

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.63
PhyloP100		-0.0030
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: rs13088006; hg19: chr3-133295185;