NM_003818.4:c.58-15579T>C

Variant names:

• chr20-5157944-T-C
• rs10485482
• NM_003818.4:c.58-15579T>C

Variant summary

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

The NM_003818.4(CDS2):​c.58-15579T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0253 in 152,244 control chromosomes in the GnomAD database, including 70 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 0.025 (70 hom., cov: 32)
• Consequence: CDS2 NM_003818.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 0 publications found

Genes affected

CDS2 (HGNC:1801): (CDP-diacylglycerol synthase 2) Breakdown products of phosphoinositides are ubiquitous second messengers that function downstream of many G protein-coupled receptors and tyrosine kinases regulating cell growth, calcium metabolism, and protein kinase C activity. This gene encodes an enzyme which regulates the amount of phosphatidylinositol available for signaling by catalyzing the conversion of phosphatidic acid to CDP-diacylglycerol. This enzyme is an integral membrane protein localized to two subcellular domains, the matrix side of the inner mitochondrial membrane where it is thought to be involved in the synthesis of phosphatidylglycerol and cardiolipin and the cytoplasmic side of the endoplasmic reticulum where it functions in phosphatidylinositol biosynthesis. Two genes encoding this enzyme have been identified in humans, one mapping to human chromosome 4q21 and a second to 20p13. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDS2	NM_003818.4	c.58-15579T>C		intron_variant	Intron 1 of 12	ENST00000460006.6	NP_003809.1
CDS2	XM_006723660.3	c.58-15579T>C		intron_variant	Intron 1 of 11		XP_006723723.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDS2	ENST00000460006.6	c.58-15579T>C		intron_variant	Intron 1 of 12	1	NM_003818.4	ENSP00000419879.1

Frequencies

GnomAD3 genomes AF: 0.0254 AC: 3858 AN: 152126 Hom.: 71 Cov.: 32

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.0712

Gnomad FIN AF: 0.0170

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0253 AC: 3858 AN: 152244 Hom.: 70 Cov.: 32 AF XY: 0.0267 AC XY: 1990 AN XY: 74444

African (AFR) AF: 0.0358 AC: 1485 AN: 41530

American (AMR) AF: 0.0259 AC: 397 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3472

East Asian (EAS) AF: 0.0807 AC: 417 AN: 5168

South Asian (SAS) AF: 0.0702 AC: 339 AN: 4828

European-Finnish (FIN) AF: 0.0170 AC: 180 AN: 10610

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0123 AC: 840 AN: 68020

Other (OTH) AF: 0.0246 AC: 52 AN: 2110

Alfa AF: 0.0194 Hom.: 26

Bravo AF: 0.0266

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.88
PhyloP100		-0.32
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: rs10485482; hg19: chr20-5138590;