Variant 8-143429783-ATGGTGGTGGTGGTGGTGG-ATGGTGGTGG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2

The NM_201589.4(MAFA):c.615_623delCCACCACCA(p.His206_His208del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000334 in 1,407,144 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00020 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00035 ( 1 hom. )

Consequence

MAFA
NM_201589.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: 5.55

Variant links:

Genes affected

MAFA (HGNC:23145): (MAF bZIP transcription factor A) MAFA is a transcription factor that binds RIPE3b, a conserved enhancer element that regulates pancreatic beta cell-specific expression of the insulin gene (INS; MIM 176730) (Olbrot et al., 2002 [PubMed 12011435]).[supplied by OMIM, Mar 2008]

MAFA links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP6

Variant 8-143429783-ATGGTGGTGG-A is Benign according to our data. Variant chr8-143429783-ATGGTGGTGG-A is described in ClinVar as [Likely_benign]. Clinvar id is 2443167.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High AC in GnomAd4 at 29 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAFA	NM_201589.4 link	c.615_623delCCACCACCA	p.His206_His208del	disruptive_inframe_deletion	Exon 1 of 1	ENST00000333480.3	NP_963883.2	Q8NHW3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAFA	ENST00000333480.3 link	c.615_623delCCACCACCA	p.His206_His208del	disruptive_inframe_deletion	Exon 1 of 1	6	NM_201589.4	ENSP00000328364.2		Q8NHW3
MAFA	ENST00000528185.1 link	n.107_115delCCACCACCA		non_coding_transcript_exon_variant	Exon 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.000197

AC:

AN:

146948

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000752

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000671

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000861

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000301

Gnomad OTH

AF:

0.000493

GnomAD3 exomes

AF:

0.000558

AC:

AN:

68082

Hom.:

AF XY:

0.000617

AC XY:

AN XY:

37262

show subpopulations

Gnomad AFR exome

AF:

0.000457

Gnomad AMR exome

AF:

0.000362

Gnomad ASJ exome

AF:

0.000667

Gnomad EAS exome

AF:

0.00146

Gnomad SAS exome

AF:

0.0000872

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000804

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000350

AC:

441

AN:

1260076

Hom.:

AF XY:

0.000354

AC XY:

219

AN XY:

619322

show subpopulations

Gnomad4 AFR exome

AF:

0.000404

Gnomad4 AMR exome

AF:

0.000464

Gnomad4 ASJ exome

AF:

0.000223

Gnomad4 EAS exome

AF:

0.000409

Gnomad4 SAS exome

AF:

0.000230

Gnomad4 FIN exome

AF:

0.0000329

Gnomad4 NFE exome

AF:

0.000357

Gnomad4 OTH exome

AF:

0.000514

GnomAD4 genome

AF:

0.000197

AC:

AN:

147068

Hom.:

Cov.:

AF XY:

0.000167

AC XY:

AN XY:

71674

show subpopulations

Gnomad4 AFR

AF:

0.0000749

Gnomad4 AMR

AF:

0.0000670

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000864

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000301

Gnomad4 OTH

AF:

0.000488

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not specified

Benign:1

Jun 09, 2022

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

MAFA-related disorder

Benign:1

Apr 28, 2022

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

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