Variant 9-13150532-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001378778.1(MPDZ):c.3609A>G(p.Lys1203Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 1,568,516 control chromosomes in the GnomAD database, including 95,194 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 14582 hom., cov: 31)

Exomes 𝑓: 0.33 ( 80612 hom. )

Consequence

MPDZ
NM_001378778.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.31

Variant links:

Genes affected

MPDZ (HGNC:7208): (multiple PDZ domain crumbs cell polarity complex component) The protein encoded by this gene has multiple PDZ domains, which are hallmarks of protein-protein interactions. The encoded protein is known to interact with the HTR2C receptor and may cause it to clump at the cell surface. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]

MPDZ links:

MPDZ (HGNC:):

MPDZ links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 9-13150532-T-C is Benign according to our data. Variant chr9-13150532-T-C is described in ClinVar as [Benign]. Clinvar id is 158891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.31 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MPDZ	NM_001378778.1 linkuse as main transcript	c.3609A>G	p.Lys1203Lys	synonymous_variant	25/47	ENST00000319217.12	NP_001365707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MPDZ	ENST00000319217.12 linkuse as main transcript	c.3609A>G	p.Lys1203Lys	synonymous_variant	25/47	5	NM_001378778.1	ENSP00000320006.7		O75970-1

Frequencies

GnomAD3 genomes

AF:

0.417

AC:

63190

AN:

151476

Hom.:

14559

Cov.:

show subpopulations

Gnomad AFR

AF:

0.620

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.403

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.403

GnomAD3 exomes

AF:

0.345

AC:

79984

AN:

232134

Hom.:

14769

AF XY:

0.343

AC XY:

43478

AN XY:

126754

show subpopulations

Gnomad AFR exome

AF:

0.619

Gnomad AMR exome

AF:

0.313

Gnomad ASJ exome

AF:

0.314

Gnomad EAS exome

AF:

0.459

Gnomad SAS exome

AF:

0.383

Gnomad FIN exome

AF:

0.284

Gnomad NFE exome

AF:

0.308

Gnomad OTH exome

AF:

0.313

GnomAD4 exome

AF:

0.331

AC:

468960

AN:

1416922

Hom.:

80612

Cov.:

AF XY:

0.331

AC XY:

233149

AN XY:

703842

show subpopulations

Gnomad4 AFR exome

AF:

0.625

Gnomad4 AMR exome

AF:

0.325

Gnomad4 ASJ exome

AF:

0.314

Gnomad4 EAS exome

AF:

0.490

Gnomad4 SAS exome

AF:

0.380

Gnomad4 FIN exome

AF:

0.280

Gnomad4 NFE exome

AF:

0.315

Gnomad4 OTH exome

AF:

0.351

GnomAD4 genome

AF:

0.417

AC:

63261

AN:

151594

Hom.:

14582

Cov.:

AF XY:

0.417

AC XY:

30864

AN XY:

74058

show subpopulations

Gnomad4 AFR

AF:

0.620

Gnomad4 AMR

AF:

0.402

Gnomad4 ASJ

AF:

0.302

Gnomad4 EAS

AF:

0.481

Gnomad4 SAS

AF:

0.395

Gnomad4 FIN

AF:

0.297

Gnomad4 NFE

AF:

0.319

Gnomad4 OTH

AF:

0.405

Alfa

AF:

0.344

Hom.:

12491

Bravo

AF:

0.431

Asia WGS

AF:

0.460

AC:

1597

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Apr 08, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

5.8

DANN

Benign

0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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