Variant chr4-15778624-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001775.4(CD38):c.210C>T(p.Tyr70=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00408 in 1,612,850 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0033 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0042 ( 23 hom. )

Consequence

CD38
NM_001775.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.513

Variant links:

Genes affected

CD38 (HGNC:1667): (CD38 molecule) The protein encoded by this gene is a non-lineage-restricted, type II transmembrane glycoprotein that synthesizes and hydrolyzes cyclic adenosine 5'-diphosphate-ribose, an intracellular calcium ion mobilizing messenger. The release of soluble protein and the ability of membrane-bound protein to become internalized indicate both extracellular and intracellular functions for the protein. This protein has an N-terminal cytoplasmic tail, a single membrane-spanning domain, and a C-terminal extracellular region with four N-glycosylation sites. Crystal structure analysis demonstrates that the functional molecule is a dimer, with the central portion containing the catalytic site. It is used as a prognostic marker for patients with chronic lymphocytic leukemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

CD38 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 4-15778624-C-T is Benign according to our data. Variant chr4-15778624-C-T is described in ClinVar as [Benign]. Clinvar id is 790390.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.513 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 23 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD38	NM_001775.4 linkuse as main transcript	c.210C>T	p.Tyr70=	synonymous_variant	1/8	ENST00000226279.8
CD38	NR_132660.2 linkuse as main transcript	n.297C>T		non_coding_transcript_exon_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD38	ENST00000226279.8 linkuse as main transcript	c.210C>T	p.Tyr70=	synonymous_variant	1/8	1	NM_001775.4	P1	P28907-1
CD38	ENST00000502843.5 linkuse as main transcript	c.210C>T	p.Tyr70=	synonymous_variant, NMD_transcript_variant	1/7	1			P28907-2
CD38	ENST00000506191.1 linkuse as main transcript	n.327C>T		non_coding_transcript_exon_variant	1/2	2
CD38	ENST00000511430.1 linkuse as main transcript	n.313C>T		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes

AF:

0.00331

AC:

503

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00128

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00406

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00506

Gnomad OTH

AF:

0.00479

GnomAD3 exomes

AF:

0.00318

AC:

795

AN:

250256

Hom.:

AF XY:

0.00334

AC XY:

452

AN XY:

135326

show subpopulations

Gnomad AFR exome

AF:

0.000988

Gnomad AMR exome

AF:

0.00179

Gnomad ASJ exome

AF:

0.00686

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000490

Gnomad FIN exome

AF:

0.00201

Gnomad NFE exome

AF:

0.00496

Gnomad OTH exome

AF:

0.00475

GnomAD4 exome

AF:

0.00416

AC:

6069

AN:

1460568

Hom.:

Cov.:

AF XY:

0.00406

AC XY:

2953

AN XY:

726592

show subpopulations

Gnomad4 AFR exome

AF:

0.000628

Gnomad4 AMR exome

AF:

0.00208

Gnomad4 ASJ exome

AF:

0.00640

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000371

Gnomad4 FIN exome

AF:

0.00175

Gnomad4 NFE exome

AF:

0.00486

Gnomad4 OTH exome

AF:

0.00398

GnomAD4 genome

AF:

0.00331

AC:

504

AN:

152282

Hom.:

Cov.:

AF XY:

0.00309

AC XY:

230

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00128

Gnomad4 AMR

AF:

0.00405

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00507

Gnomad4 OTH

AF:

0.00474

Alfa

AF:

0.00441

Hom.:

Bravo

AF:

0.00337

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00534

EpiControl

AF:

0.00504

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

6.3

DANN

Benign

0.88

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over