Variant chr16-29810108-AGCGGCAGCG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2

The NM_002383.4(MAZ):c.1323_1331del(p.Ala446_Ala448del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00287 in 1,542,868 control chromosomes in the GnomAD database, including 20 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 18 hom. )

Consequence

MAZ
NM_002383.4 inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.70

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.

BP3

Nonframeshift variant in repetitive region in NM_002383.4

BP6

Variant 16-29810108-AGCGGCAGCG-A is Benign according to our data. Variant chr16-29810108-AGCGGCAGCG-A is described in ClinVar as [Likely_benign]. Clinvar id is 2646368.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00283 (3960/1397548) while in subpopulation MID AF= 0.023 (118/5138). AF 95% confidence interval is 0.0196. There are 18 homozygotes in gnomad4_exome. There are 1984 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

BS2

High AC in GnomAd4 at 463 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAZ	NM_002383.4 linkuse as main transcript	c.1323_1331del	p.Ala446_Ala448del	inframe_deletion	5/5	ENST00000322945.11
LOC112268170	XM_047435008.1 linkuse as main transcript	c.1388_1396del		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.1323_1331del	p.Ala446_Ala448del	inframe_deletion	5/5	1	NM_002383.4		P56270-1
MVP-DT	ENST00000569039.5 linkuse as main transcript	n.302_310del		non_coding_transcript_exon_variant	3/4	2

Frequencies

GnomAD3 genomes

AF:

0.00320

AC:

464

AN:

145194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00321

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00617

Gnomad ASJ

AF:

0.00447

Gnomad EAS

AF:

0.00861

Gnomad SAS

AF:

0.00250

Gnomad FIN

AF:

0.000949

Gnomad MID

AF:

0.0175

Gnomad NFE

AF:

0.00244

Gnomad OTH

AF:

0.00299

GnomAD3 exomes

AF:

0.00380

AC:

925

AN:

243396

Hom.:

AF XY:

0.00374

AC XY:

499

AN XY:

133280

show subpopulations

Gnomad AFR exome

AF:

0.00353

Gnomad AMR exome

AF:

0.00427

Gnomad ASJ exome

AF:

0.00592

Gnomad EAS exome

AF:

0.00774

Gnomad SAS exome

AF:

0.00306

Gnomad FIN exome

AF:

0.000611

Gnomad NFE exome

AF:

0.00363

Gnomad OTH exome

AF:

0.00474

GnomAD4 exome

AF:

0.00283

AC:

3960

AN:

1397548

Hom.:

AF XY:

0.00287

AC XY:

1984

AN XY:

692010

show subpopulations

Gnomad4 AFR exome

AF:

0.00437

Gnomad4 AMR exome

AF:

0.00432

Gnomad4 ASJ exome

AF:

0.00597

Gnomad4 EAS exome

AF:

0.00411

Gnomad4 SAS exome

AF:

0.00377

Gnomad4 FIN exome

AF:

0.00117

Gnomad4 NFE exome

AF:

0.00246

Gnomad4 OTH exome

AF:

0.00432

GnomAD4 genome

AF:

0.00319

AC:

463

AN:

145320

Hom.:

Cov.:

AF XY:

0.00299

AC XY:

212

AN XY:

70966

show subpopulations

Gnomad4 AFR

AF:

0.00320

Gnomad4 AMR

AF:

0.00609

Gnomad4 ASJ

AF:

0.00447

Gnomad4 EAS

AF:

0.00863

Gnomad4 SAS

AF:

0.00250

Gnomad4 FIN

AF:

0.000949

Gnomad4 NFE

AF:

0.00244

Gnomad4 OTH

AF:

0.00296

Alfa

AF:

0.0000849

Hom.:

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

Feb 01, 2023

MAZ: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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