rs889695

Variant names:

• chr16-29863614-T-C
• rs889695
• ENST00000565014.6:n.67T>C

Variant summary

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

The ENST00000565014.6(CDIPTOSP):​n.67T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,208 control chromosomes in the GnomAD database, including 8,670 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 0.32 (8662 hom., cov: 31)
  • Exomes 𝑓: 0.28 (8 hom.)
• Consequence: CDIPTOSP ENST00000565014.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 13 publications found

Genes affected

CDIPTOSP (HGNC:):

CDIPT (HGNC:1769): (CDP-diacylglycerol--inositol 3-phosphatidyltransferase) Phosphatidylinositol breakdown products 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. Two enzymes, CDP-diacylglycerol synthase and phosphatidylinositol synthase, are involved in the biosynthesis of phosphatidylinositol. Phosphatidylinositol synthase, a member of the CDP-alcohol phosphatidyl transferase class-I family, is an integral membrane protein found on the cytoplasmic side of the endoplasmic reticulum and the Golgi apparatus. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

CDIPTOSP (HGNC:48609): (CDIP transferase opposite strand, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565014.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDIPTOSP	NR_015396.1		n.-220T>C		upstream_gene	N/A
	CDIPTOSP	NR_024370.1		n.-69T>C		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDIPTOSP	ENST00000565014.6	TSL:2	n.67T>C		non_coding_transcript_exon	Exon 1 of 6
	CDIPTOSP	ENST00000790396.1		n.66T>C		non_coding_transcript_exon	Exon 1 of 6
	CDIPTOSP	ENST00000790397.1		n.64T>C		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48844 AN: 151794 Hom.: 8632 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.268

GnomAD4 exome AF: 0.277 AC: 82 AN: 296 Hom.: 8 Cov.: 0 AF XY: 0.275 AC XY: 61 AN XY: 222

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.290 AC: 54 AN: 186

European-Finnish (FIN) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.256 AC: 23 AN: 90

Other (OTH) AF: 0.250 AC: 3 AN: 12

GnomAD4 genome AF: 0.322 AC: 48916 AN: 151912 Hom.: 8662 Cov.: 31 AF XY: 0.317 AC XY: 23527 AN XY: 74236

African (AFR) AF: 0.468 AC: 19381 AN: 41406

American (AMR) AF: 0.195 AC: 2984 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 803 AN: 3466

East Asian (EAS) AF: 0.119 AC: 616 AN: 5160

South Asian (SAS) AF: 0.203 AC: 979 AN: 4818

European-Finnish (FIN) AF: 0.301 AC: 3181 AN: 10562

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20130 AN: 67926

Other (OTH) AF: 0.265 AC: 556 AN: 2102

Alfa AF: 0.327 Hom.: 1343

Bravo AF: 0.319

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.2
DANN	Benign	0.61
PhyloP100		-0.071
PromoterAI		0.026	Neutral
Mutation Taster		=300/0	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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs889695;

hg19: chr16-29874935;