dbSNP rs141816879: MAFA:p.His202_His208del (chr8-143429783-ATGGTGGTGGTGGTGGTGGTGG-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_201589.4(MAFA):c.603_623delCCACCACCACCACCACCACCA(p.His202_His208del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000396 in 1,262,476 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.0000040 ( 0 hom. )

Consequence

MAFA
NM_201589.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.55

Publications

0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAdExome4 at 5 AD gene.

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.603_623delCCACCACCACCACCACCACCA	p.His202_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.603_623delCCACCACCACCACCACCACCA	p.His202_His208del	disruptive_inframe_deletion	Exon 1 of 1	ENSP00000328364.2	Q8NHW3
	MAFA	ENST00000528185.1	TSL:3	n.95_115delCCACCACCACCACCACCACCA		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000396

AC:

AN:

1262476

Hom.:

AF XY:

0.00000161

AC XY:

AN XY:

620548

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

27250

American (AMR)

AF:

0.00

AC:

AN:

30288

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22526

East Asian (EAS)

AF:

0.0000340

AC:

AN:

29398

South Asian (SAS)

AF:

0.00

AC:

AN:

69600

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30516

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3710

European-Non Finnish (NFE)

AF:

0.00000201

AC:

AN:

996564

Other (OTH)

AF:

0.0000380

AC:

AN:

52624

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

5.5

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over