Genetic Variant NM_201589.4:c.618_623delCCACCA (chr8-143429783-ATGGTGG-A) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP6BA1

The NM_201589.4(MAFA):c.618_623delCCACCA(p.His207_His208del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.105 in 1,041,888 control chromosomes in the GnomAD database, including 3,246 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.059 ( 345 hom., cov: 0)

Exomes 𝑓: 0.11 ( 2901 hom. )

Consequence

MAFA
NM_201589.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 5.55

Publications

12 publications found

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 was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP6

Variant 8-143429783-ATGGTGG-A is Benign according to our data. Variant chr8-143429783-ATGGTGG-A is described in ClinVar as Benign. ClinVar VariationId is 3055523.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0804 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201589.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAFA	NM_201589.4	MANE Select	c.618_623delCCACCA	p.His207_His208del	disruptive_inframe_deletion	Exon 1 of 1	NP_963883.2	Q8NHW3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAFA	ENST00000333480.3	TSL:6 MANE Select	c.618_623delCCACCA	p.His207_His208del	disruptive_inframe_deletion	Exon 1 of 1	ENSP00000328364.2	Q8NHW3
	MAFA	ENST00000528185.1	TSL:3	n.110_115delCCACCA		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0590

AC:

8648

AN:

146588

Hom.:

345

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0321

Gnomad AMI

AF:

0.0203

Gnomad AMR

AF:

0.0553

Gnomad ASJ

AF:

0.0998

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0128

Gnomad FIN

AF:

0.0517

Gnomad MID

AF:

0.0691

Gnomad NFE

AF:

0.0822

Gnomad OTH

AF:

0.0743

GnomAD2 exomes

AF:

0.114

AC:

7749

AN:

68082

AF XY:

0.114

show subpopulations

Gnomad AFR exome

AF:

0.0630

Gnomad AMR exome

AF:

0.0934

Gnomad ASJ exome

AF:

0.176

Gnomad EAS exome

AF:

0.0471

Gnomad FIN exome

AF:

0.127

Gnomad NFE exome

AF:

0.149

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.113

AC:

101200

AN:

895184

Hom.:

2901

AF XY:

0.113

AC XY:

49285

AN XY:

436250

show subpopulations

African (AFR)

AF:

0.0499

AC:

1059

AN:

21210

American (AMR)

AF:

0.0988

AC:

2091

AN:

21154

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

2496

AN:

15300

East Asian (EAS)

AF:

0.0199

AC:

351

AN:

17634

South Asian (SAS)

AF:

0.0488

AC:

2039

AN:

41758

European-Finnish (FIN)

AF:

0.116

AC:

1992

AN:

17158

Middle Eastern (MID)

AF:

0.123

AC:

320

AN:

2592

European-Non Finnish (NFE)

AF:

0.120

AC:

86843

AN:

721932

Other (OTH)

AF:

0.110

AC:

4009

AN:

36446

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

6106

12212

18317

24423

30529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3162

6324

9486

12648

15810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0589

AC:

8647

AN:

146704

Hom.:

345

Cov.:

AF XY:

0.0563

AC XY:

4023

AN XY:

71456

show subpopulations

African (AFR)

AF:

0.0321

AC:

1283

AN:

40002

American (AMR)

AF:

0.0552

AC:

821

AN:

14872

Ashkenazi Jewish (ASJ)

AF:

0.0998

AC:

341

AN:

3418

East Asian (EAS)

AF:

0.00

AC:

AN:

4624

South Asian (SAS)

AF:

0.0128

AC:

AN:

4516

European-Finnish (FIN)

AF:

0.0517

AC:

503

AN:

9724

Middle Eastern (MID)

AF:

0.0634

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.0822

AC:

5455

AN:

66336

Other (OTH)

AF:

0.0735

AC:

150

AN:

2042

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

395

789

1184

1578

1973

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.162

Hom.:

4374

ClinVar

ClinVar submissions

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

MAFA-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

5.5

Mutation Taster

=153/47

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over