16-29810108-AGCGGCAGCG-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2
The NM_002383.4(MAZ):βc.1323_1331delβ(p.Ala446_Ala448del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00287 in 1,542,868 control chromosomes in the GnomAD database, including 20 homozygotes. Variant has been reported in ClinVar as Likely benign (β ).
Frequency
Genomes: π 0.0032 ( 2 hom., cov: 32)
Exomes π: 0.0028 ( 18 hom. )
Consequence
MAZ
NM_002383.4 inframe_deletion
NM_002383.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.70
Genes affected
MAZ (HGNC:6914): (MYC associated zinc finger protein) Enables DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including regulation of gene expression; regulation of signal transduction; and transcription by RNA polymerase II. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_002383.4
BP6
Variant 16-29810108-AGCGGCAGCG-A is Benign according to our data. Variant chr16-29810108-AGCGGCAGCG-A is described in ClinVar as [Likely_benign]. Clinvar id is 2646368.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00283 (3960/1397548) while in subpopulation MID AF= 0.023 (118/5138). AF 95% confidence interval is 0.0196. There are 18 homozygotes in gnomad4_exome. There are 1984 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High AC in GnomAd4 at 463 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAZ | NM_002383.4 | c.1323_1331del | p.Ala446_Ala448del | inframe_deletion | 5/5 | ENST00000322945.11 | |
LOC112268170 | XM_047435008.1 | c.*1388_*1396del | 3_prime_UTR_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAZ | ENST00000322945.11 | c.1323_1331del | p.Ala446_Ala448del | inframe_deletion | 5/5 | 1 | NM_002383.4 | ||
MVP-DT | ENST00000569039.5 | n.302_310del | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00320 AC: 464AN: 145194Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00380 AC: 925AN: 243396Hom.: 4 AF XY: 0.00374 AC XY: 499AN XY: 133280
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GnomAD4 exome AF: 0.00283 AC: 3960AN: 1397548Hom.: 18 AF XY: 0.00287 AC XY: 1984AN XY: 692010
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GnomAD4 genome AF: 0.00319 AC: 463AN: 145320Hom.: 2 Cov.: 32 AF XY: 0.00299 AC XY: 212AN XY: 70966
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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 | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | MAZ: BS2 - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at