rs141816879

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-143429783-ATGGTGGTGGTGGTGGTGG-A
• chr8-143429783-ATGGTGGTGGTGGTGGTGG-ATGG
• chr8-143429783-ATGGTGGTGGTGGTGGTGG-ATGGTGG
• chr8-143429783-ATGGTGGTGGTGGTGGTGG-ATGGTGGTGG
• chr8-143429783-ATGGTGGTGGTGGTGGTGG-ATGGTGGTGGTGG
• chr8-143429783-ATGGTGGTGGTGGTGGTGG-ATGGTGGTGGTGGTGG
• chr8-143429783-ATGGTGGTGGTGGTGGTGG-ATGGTGGTGGTGGTGGTGGTGG
• chr8-143429783-ATGGTGGTGGTGGTGGTGG-ATGGTGGTGGTGGTGGTGGTGGTGG
• chr8-143429783-ATGGTGGTGGTGGTGGTGG-ATGGTGGTGGTGGTGGTGGTGGTGGTGG
• chr8-143429783-ATGGTGGTGGTGGTGGTGG-ATGGTGGTGGTGGTGGTGGTGGTGGTGGTGG

Variant summary

Our verdict is Likely benign. Variant got -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. 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

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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 12 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAFA	NM_201589.4	c.606_623delCCACCACCACCACCACCA	p.His203_His208del	disruptive_inframe_deletion	Exon 1 of 1	ENST00000333480.3	NP_963883.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAFA	ENST00000333480.3	c.606_623delCCACCACCACCACCACCA	p.His203_His208del	disruptive_inframe_deletion	Exon 1 of 1	6	NM_201589.4	ENSP00000328364.2
MAFA	ENST00000528185.1	n.98_115delCCACCACCACCACCACCA		non_coding_transcript_exon_variant	Exon 1 of 2	3

Frequencies

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

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000144

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000110

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs141816879; hg19: chr8-144511953;