chr8-143430014-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_201589.4(MAFA):c.393C>T(p.Leu131=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00526 in 1,373,712 control chromosomes in the GnomAD database, including 285 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.027 ( 172 hom., cov: 30)
Exomes 𝑓: 0.0026 ( 113 hom. )
Consequence
MAFA
NM_201589.4 synonymous
NM_201589.4 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 1.08
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 Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 8-143430014-G-A is Benign according to our data. Variant chr8-143430014-G-A is described in ClinVar as [Benign]. Clinvar id is 3056164.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.08 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0898 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAFA | NM_201589.4 | c.393C>T | p.Leu131= | synonymous_variant | 1/1 | ENST00000333480.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAFA | ENST00000333480.3 | c.393C>T | p.Leu131= | synonymous_variant | 1/1 | NM_201589.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0271 AC: 4042AN: 149358Hom.: 171 Cov.: 30
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GnomAD3 exomes AF: 0.00415 AC: 386AN: 93000Hom.: 12 AF XY: 0.00268 AC XY: 145AN XY: 54030
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GnomAD4 exome AF: 0.00259 AC: 3174AN: 1224246Hom.: 113 Cov.: 34 AF XY: 0.00230 AC XY: 1390AN XY: 604170
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GnomAD4 genome AF: 0.0271 AC: 4053AN: 149466Hom.: 172 Cov.: 30 AF XY: 0.0263 AC XY: 1918AN XY: 72880
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MAFA-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 06, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Uncertain
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at