GeneBe

rs141816879

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS2

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. 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
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BS2
High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAFANM_201589.4 linkc.603_623delCCACCACCACCACCACCACCA p.His202_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
MAFAENST00000333480.3 linkc.603_623delCCACCACCACCACCACCACCA p.His202_His208del disruptive_inframe_deletion Exon 1 of 1 6 NM_201589.4 ENSP00000328364.2 Q8NHW3
MAFAENST00000528185.1 linkn.95_115delCCACCACCACCACCACCACCA non_coding_transcript_exon_variant Exon 1 of 2 3

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000396
AC:
5
AN:
1262476
Hom.:
0
AF XY:
0.00000161
AC XY:
1
AN XY:
620548
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000340
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000201
Gnomad4 OTH exome
AF:
0.0000380
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-144511953; API