16-79598718-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_005360.5(MAF):c.1118+67T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,605,716 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0060 ( 14 hom., cov: 29)
Exomes 𝑓: 0.00070 ( 12 hom. )
Consequence
MAF
NM_005360.5 intron
NM_005360.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.13
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
?
Variant 16-79598718-A-G is Benign according to our data. Variant chr16-79598718-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1217576.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00603 (915/151766) while in subpopulation AFR AF= 0.0211 (872/41308). AF 95% confidence interval is 0.0199. There are 14 homozygotes in gnomad4. There are 419 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
?
High AC in GnomAd at 915 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAF | NM_005360.5 | c.1118+67T>C | intron_variant | ENST00000326043.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAF | ENST00000326043.5 | c.1118+67T>C | intron_variant | 1 | NM_005360.5 | A2 | |||
MAF | ENST00000393350.1 | c.*63T>C | 3_prime_UTR_variant | 1/1 | A2 | ||||
MAF | ENST00000569649.1 | c.1118+67T>C | intron_variant | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00603 AC: 915AN: 151648Hom.: 14 Cov.: 29
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GnomAD4 exome AF: 0.000703 AC: 1022AN: 1453950Hom.: 12 Cov.: 37 AF XY: 0.000623 AC XY: 450AN XY: 722584
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 21, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at