chr8-143429938-GGTGGTGCGCGCC-G
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM4PP3BP6_ModerateBS2
The NM_201589.4(MAFA):βc.457_468delβ(p.Gly153_His156del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,261,612 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (β ).
Frequency
Genomes: π 0.0040 ( 0 hom., cov: 29)
Exomes π: 0.0014 ( 3 hom. )
Consequence
MAFA
NM_201589.4 inframe_deletion
NM_201589.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.56
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 -3 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_201589.4.
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
BP6
Variant 8-143429938-GGTGGTGCGCGCC-G is Benign according to our data. Variant chr8-143429938-GGTGGTGCGCGCC-G is described in ClinVar as [Likely_benign]. Clinvar id is 1336038.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 587 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAFA | NM_201589.4 | c.457_468del | p.Gly153_His156del | inframe_deletion | 1/1 | ENST00000333480.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAFA | ENST00000333480.3 | c.457_468del | p.Gly153_His156del | inframe_deletion | 1/1 | NM_201589.4 | P1 | ||
MAFA | ENST00000528185.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00398 AC: 588AN: 147812Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.00145 AC: 19AN: 13136Hom.: 0 AF XY: 0.00137 AC XY: 12AN XY: 8732
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GnomAD4 exome AF: 0.00142 AC: 1586AN: 1113680Hom.: 3 AF XY: 0.00133 AC XY: 716AN XY: 536558
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GnomAD4 genome AF: 0.00397 AC: 587AN: 147932Hom.: 0 Cov.: 29 AF XY: 0.00400 AC XY: 288AN XY: 72080
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 03, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at