16-79598601-T-TGTGC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_005360.5(MAF):c.1118+183_1118+184insGCAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 1,482,918 control chromosomes in the GnomAD database, including 215 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.022 ( 53 hom., cov: 25)
Exomes 𝑓: 0.028 ( 162 hom. )
Consequence
MAF
NM_005360.5 intron
NM_005360.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.31
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 -10 ACMG points.
BP6
?
Variant 16-79598601-T-TGTGC is Benign according to our data. Variant chr16-79598601-T-TGTGC is described in ClinVar as [Likely_benign]. Clinvar id is 1202104.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0219 (3150/143796) while in subpopulation AMR AF= 0.0307 (434/14156). AF 95% confidence interval is 0.0283. There are 53 homozygotes in gnomad4. There are 1532 alleles in male gnomad4 subpopulation. Median coverage is 25. This position pass quality control queck.
BS2
?
High AC in GnomAd at 3153 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAF | NM_005360.5 | c.1118+183_1118+184insGCAC | intron_variant | ENST00000326043.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAF | ENST00000326043.5 | c.1118+183_1118+184insGCAC | intron_variant | 1 | NM_005360.5 | A2 | |||
MAF | ENST00000393350.1 | c.*179_*180insGCAC | 3_prime_UTR_variant | 1/1 | A2 | ||||
MAF | ENST00000569649.1 | c.1118+183_1118+184insGCAC | intron_variant | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0219 AC: 3153AN: 143708Hom.: 53 Cov.: 25
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GnomAD4 exome AF: 0.0276 AC: 36914AN: 1339122Hom.: 162 Cov.: 56 AF XY: 0.0273 AC XY: 17866AN XY: 655278
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GnomAD4 genome ? AF: 0.0219 AC: 3150AN: 143796Hom.: 53 Cov.: 25 AF XY: 0.0220 AC XY: 1532AN XY: 69678
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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 | Oct 02, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at