Variant 9-13192321-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001378778.1(MPDZ):c.1804-26G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.991 in 1,567,236 control chromosomes in the GnomAD database, including 770,529 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.98 ( 73592 hom., cov: 32)

Exomes 𝑓: 0.99 ( 696937 hom. )

Consequence

MPDZ
NM_001378778.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0450

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 9-13192321-C-G is Benign according to our data. Variant chr9-13192321-C-G is described in ClinVar as [Benign]. Clinvar id is 1321175.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPDZ	NM_001378778.1 linkuse as main transcript	c.1804-26G>C		intron_variant		ENST00000319217.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPDZ	ENST00000319217.12 linkuse as main transcript	c.1804-26G>C		intron_variant		5	NM_001378778.1	A1	O75970-1

Frequencies

GnomAD3 genomes

AF:

0.983

AC:

149539

AN:

152156

Hom.:

73532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.955

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.992

Gnomad ASJ

AF:

0.993

Gnomad EAS

AF:

0.995

Gnomad SAS

AF:

0.922

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.984

Gnomad NFE

AF:

0.998

Gnomad OTH

AF:

0.981

GnomAD3 exomes

AF:

0.983

AC:

183932

AN:

187116

Hom.:

90483

AF XY:

0.980

AC XY:

97547

AN XY:

99548

show subpopulations

Gnomad AFR exome

AF:

0.952

Gnomad AMR exome

AF:

0.991

Gnomad ASJ exome

AF:

0.993

Gnomad EAS exome

AF:

0.997

Gnomad SAS exome

AF:

0.918

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

0.997

Gnomad OTH exome

AF:

0.987

GnomAD4 exome

AF:

0.992

AC:

1404019

AN:

1414962

Hom.:

696937

Cov.:

AF XY:

0.990

AC XY:

693059

AN XY:

699900

show subpopulations

Gnomad4 AFR exome

AF:

0.951

Gnomad4 AMR exome

AF:

0.991

Gnomad4 ASJ exome

AF:

0.994

Gnomad4 EAS exome

AF:

0.998

Gnomad4 SAS exome

AF:

0.923

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.998

Gnomad4 OTH exome

AF:

0.988

GnomAD4 genome

AF:

0.983

AC:

149658

AN:

152274

Hom.:

73592

Cov.:

AF XY:

0.982

AC XY:

73102

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.955

Gnomad4 AMR

AF:

0.992

Gnomad4 ASJ

AF:

0.993

Gnomad4 EAS

AF:

0.996

Gnomad4 SAS

AF:

0.922

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.998

Gnomad4 OTH

AF:

0.982

Alfa

AF:

0.993

Hom.:

8482

Bravo

AF:

0.983

Asia WGS

AF:

0.952

AC:

3310

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Hydrocephalus, nonsyndromic, autosomal recessive 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.1

DANN

Benign

0.62

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