8-143429783-ATGGTGGTGGTGGTGGTGGTGG-ATGG

Variant names:

• chr8-143429783-ATGGTGGTGGTGGTGGTGG-A
• rs141816879
• NM_201589.4:c.606_623delCCACCACCACCACCACCA

Variant summary

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

The NM_201589.4(MAFA):​c.606_623delCCACCACCACCACCACCA​(p.His203_His208del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000951 in 1,262,474 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: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000095 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MAFA NM_201589.4 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.55
• Publications: 12 publications found

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]

ACMG classification

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

• BS2: High AC in GnomAdExome4 at 12 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.606_623delCCACCACCACCACCACCA	p.His203_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.606_623delCCACCACCACCACCACCA	p.His203_His208del	disruptive_inframe_deletion	Exon 1 of 1	ENSP00000328364.2	Q8NHW3
	MAFA	ENST00000528185.1	TSL:3	n.98_115delCCACCACCACCACCACCA		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 146952 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000951 AC: 12 AN: 1262474 Hom.: 0 AF XY: 0.0000145 AC XY: 9 AN XY: 620546

African (AFR) AF: 0.00 AC: 0 AN: 27250

American (AMR) AF: 0.00 AC: 0 AN: 30286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22526

East Asian (EAS) AF: 0.00 AC: 0 AN: 29398

South Asian (SAS) AF: 0.0000144 AC: 1 AN: 69600

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30516

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3710

European-Non Finnish (NFE) AF: 0.0000110 AC: 11 AN: 996564

Other (OTH) AF: 0.00 AC: 0 AN: 52624

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 146952 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 71552

African (AFR) AF: 0.00 AC: 0 AN: 39916

American (AMR) AF: 0.00 AC: 0 AN: 14904

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3424

East Asian (EAS) AF: 0.00 AC: 0 AN: 4648

South Asian (SAS) AF: 0.00 AC: 0 AN: 4522

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9836

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 304

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66482

Other (OTH) AF: 0.00 AC: 0 AN: 2028

Alfa AF: 0.00 Hom.: 4374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.5
Mutation Taster		=149/51	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs141816879; hg19: chr8-144511953;