dbSNP rs889695: CDIPTOSP:n.67T>C (chr16-29863614-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0710

Publications

13 publications found

Variant links:

Genes affected

CDIPTOSP (HGNC:):

CDIPTOSP links:

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]

CDIPT links:

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

CDIPTOSP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDIPTOSP	NR_015396.1 link	n.-220T>C		upstream_gene_variant
CDIPTOSP	NR_024370.1 link	n.-69T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CDIPTOSP	ENST00000565014.6 link	n.67T>C	non_coding_transcript_exon_variant	Exon 1 of 6	2
CDIPTOSP	ENST00000790396.1 link	n.66T>C	non_coding_transcript_exon_variant	Exon 1 of 6
CDIPTOSP	ENST00000790397.1 link	n.64T>C	non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

48844

AN:

151794

Hom.:

8632

Cov.:

show subpopulations

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:

AN:

296

Hom.:

Cov.:

AF XY:

0.275

AC XY:

AN XY:

222

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.290

AC:

AN:

186

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.256

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.322

AC:

48916

AN:

151912

Hom.:

8662

Cov.:

AF XY:

0.317

AC XY:

23527

AN XY:

74236

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.296

AC:

20130

AN:

67926

Other (OTH)

AF:

0.265

AC:

556

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1634

3269

4903

6538

8172

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

9.2

(source)

DANN

Benign

0.61

PhyloP100

-0.071

PromoterAI

0.026

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over