16-29810108-AGCGGCAGCG-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2

The NM_002383.4(MAZ):​c.1323_1331del​(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: 𝑓 0.0032 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 18 hom. )

Consequence

MAZ
NM_002383.4 inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.70
Variant links:
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]
MVP-DT (HGNC:56029): (MVP divergent transcript)

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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
MAZNM_002383.4 linkuse as main transcriptc.1323_1331del p.Ala446_Ala448del inframe_deletion 5/5 ENST00000322945.11
LOC112268170XM_047435008.1 linkuse as main transcriptc.*1388_*1396del 3_prime_UTR_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAZENST00000322945.11 linkuse as main transcriptc.1323_1331del p.Ala446_Ala448del inframe_deletion 5/51 NM_002383.4 P56270-1
MVP-DTENST00000569039.5 linkuse as main transcriptn.302_310del non_coding_transcript_exon_variant 3/42

Frequencies

GnomAD3 genomes
AF:
0.00320
AC:
464
AN:
145194
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00321
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00617
Gnomad ASJ
AF:
0.00447
Gnomad EAS
AF:
0.00861
Gnomad SAS
AF:
0.00250
Gnomad FIN
AF:
0.000949
Gnomad MID
AF:
0.0175
Gnomad NFE
AF:
0.00244
Gnomad OTH
AF:
0.00299
GnomAD3 exomes
AF:
0.00380
AC:
925
AN:
243396
Hom.:
4
AF XY:
0.00374
AC XY:
499
AN XY:
133280
show subpopulations
Gnomad AFR exome
AF:
0.00353
Gnomad AMR exome
AF:
0.00427
Gnomad ASJ exome
AF:
0.00592
Gnomad EAS exome
AF:
0.00774
Gnomad SAS exome
AF:
0.00306
Gnomad FIN exome
AF:
0.000611
Gnomad NFE exome
AF:
0.00363
Gnomad OTH exome
AF:
0.00474
GnomAD4 exome
AF:
0.00283
AC:
3960
AN:
1397548
Hom.:
18
AF XY:
0.00287
AC XY:
1984
AN XY:
692010
show subpopulations
Gnomad4 AFR exome
AF:
0.00437
Gnomad4 AMR exome
AF:
0.00432
Gnomad4 ASJ exome
AF:
0.00597
Gnomad4 EAS exome
AF:
0.00411
Gnomad4 SAS exome
AF:
0.00377
Gnomad4 FIN exome
AF:
0.00117
Gnomad4 NFE exome
AF:
0.00246
Gnomad4 OTH exome
AF:
0.00432
GnomAD4 genome
AF:
0.00319
AC:
463
AN:
145320
Hom.:
2
Cov.:
32
AF XY:
0.00299
AC XY:
212
AN XY:
70966
show subpopulations
Gnomad4 AFR
AF:
0.00320
Gnomad4 AMR
AF:
0.00609
Gnomad4 ASJ
AF:
0.00447
Gnomad4 EAS
AF:
0.00863
Gnomad4 SAS
AF:
0.00250
Gnomad4 FIN
AF:
0.000949
Gnomad4 NFE
AF:
0.00244
Gnomad4 OTH
AF:
0.00296
Alfa
AF:
0.0000849
Hom.:
0

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2023MAZ: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1555501536; hg19: chr16-29821429; API