Variant 16-29810132-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_002383.4(MAZ):c.1335A>G(p.Ala445=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000995 in 1,607,766 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00075 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0010 ( 2 hom. )

Consequence

MAZ
NM_002383.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.12

Variant links:

Genes affected

MAZ (HGNC:6914): (MYC associated zinc finger protein) Enables DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including regulation of gene expression; regulation of signal transduction; and transcription by RNA polymerase II. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MAZ links:

LOC112268170 (HGNC:):

LOC112268170 links:

MVP-DT (HGNC:56029): (MVP divergent transcript)

MVP-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0040216744).

BP6

Variant 16-29810132-A-G is Benign according to our data. Variant chr16-29810132-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2646369.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.12 with no splicing effect.

BS2

High AC in GnomAd4 at 114 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAZ	NM_002383.4 linkuse as main transcript	c.1335A>G	p.Ala445=	synonymous_variant	5/5	ENST00000322945.11
LOC112268170	XM_047435008.1 linkuse as main transcript	c.*1373T>C		3_prime_UTR_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAZ	ENST00000322945.11 linkuse as main transcript	c.1335A>G	p.Ala445=	synonymous_variant	5/5	1	NM_002383.4		P56270-1
MVP-DT	ENST00000569039.5 linkuse as main transcript	n.287T>C		non_coding_transcript_exon_variant	3/4	2

Frequencies

GnomAD3 genomes

AF:

0.000754

AC:

114

AN:

151270

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000682

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000263

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00273

Gnomad SAS

AF:

0.000209

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000989

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000839

AC:

202

AN:

240634

Hom.:

AF XY:

0.000703

AC XY:

AN XY:

132368

show subpopulations

Gnomad AFR exome

AF:

0.000856

Gnomad AMR exome

AF:

0.000234

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00276

Gnomad SAS exome

AF:

0.000197

Gnomad FIN exome

AF:

0.0000953

Gnomad NFE exome

AF:

0.00113

Gnomad OTH exome

AF:

0.000513

GnomAD4 exome

AF:

0.00102

AC:

1485

AN:

1456376

Hom.:

Cov.:

AF XY:

0.000944

AC XY:

684

AN XY:

724486

show subpopulations

Gnomad4 AFR exome

AF:

0.000570

Gnomad4 AMR exome

AF:

0.000247

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00373

Gnomad4 SAS exome

AF:

0.000186

Gnomad4 FIN exome

AF:

0.0000958

Gnomad4 NFE exome

AF:

0.00113

Gnomad4 OTH exome

AF:

0.000532

GnomAD4 genome

AF:

0.000753

AC:

114

AN:

151390

Hom.:

Cov.:

AF XY:

0.000689

AC XY:

AN XY:

74006

show subpopulations

Gnomad4 AFR

AF:

0.000680

Gnomad4 AMR

AF:

0.000263

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00274

Gnomad4 SAS

AF:

0.000209

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000989

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00106

Hom.:

ESP6500AA

AF:

0.000519

AC:

ESP6500EA

AF:

0.000880

AC:

ExAC

AF:

0.000975

AC:

117

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

MAZ: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Benign

-0.44

CADD

Benign

0.076

DANN

Benign

0.57

FATHMM_MKL

Benign

0.0085

LIST_S2

Benign

0.20

T;T

M_CAP

Benign

0.0067

MetaRNN

Benign

0.0040

T;T

MutationTaster

Benign

1.0

N;N;N;N;N;N;N;N

PROVEAN

Benign

0.71

.;N

Sift

Pathogenic

0.0

.;D

Sift4G

Benign

0.22

T;T

Vest4

0.087

MVP

0.30

GERP RS

-6.5

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