rs140303158
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_005360.5(MAF):c.882G>A(p.Arg294=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000884 in 1,613,618 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00061 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00091 ( 3 hom. )
Consequence
MAF
NM_005360.5 synonymous
NM_005360.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.14
Genes affected
MAF (HGNC:6776): (MAF bZIP transcription factor) The protein encoded by this gene is a DNA-binding, leucine zipper-containing transcription factor that acts as a homodimer or as a heterodimer. Depending on the binding site and binding partner, the encoded protein can be a transcriptional activator or repressor. This protein plays a role in the regulation of several cellular processes, including embryonic lens fiber cell development, increased T-cell susceptibility to apoptosis, and chondrocyte terminal differentiation. Defects in this gene are a cause of juvenile-onset pulverulent cataract as well as congenital cerulean cataract 4 (CCA4). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]
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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=-0.41).
BP6
?
Variant 16-79599021-C-T is Benign according to our data. Variant chr16-79599021-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 259754.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=3.14 with no splicing effect.
BS2
?
High AC in GnomAd4 at 92 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAF | NM_005360.5 | c.882G>A | p.Arg294= | synonymous_variant | 1/2 | ENST00000326043.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAF | ENST00000326043.5 | c.882G>A | p.Arg294= | synonymous_variant | 1/2 | 1 | NM_005360.5 | A2 | |
MAF | ENST00000569649.1 | c.882G>A | p.Arg294= | synonymous_variant | 1/2 | 5 | P4 | ||
MAF | ENST00000393350.1 | c.882G>A | p.Arg294= | synonymous_variant | 1/1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000606 AC: 92AN: 151902Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.000658 AC: 164AN: 249136Hom.: 1 AF XY: 0.000615 AC XY: 83AN XY: 135046
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GnomAD4 exome AF: 0.000913 AC: 1334AN: 1461600Hom.: 3 Cov.: 36 AF XY: 0.000901 AC XY: 655AN XY: 727084
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GnomAD4 genome ? AF: 0.000605 AC: 92AN: 152018Hom.: 0 Cov.: 30 AF XY: 0.000484 AC XY: 36AN XY: 74314
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Ayme-Gripp syndrome;C1857768:Cataract 21 multiple types Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at