16-29806735-C-G

Variant names:

• chr16-29806735-C-G
• rs530190319
• NM_002383.4:c.34C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002383.4(MAZ):​c.34C>G​(p.Pro12Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000161 in 1,242,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: MAZ NM_002383.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

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]

ENSG00000259952 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.095912814).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAZ	NM_002383.4	c.34C>G	p.Pro12Ala	missense_variant	Exon 1 of 5	ENST00000322945.11	NP_002374.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAZ	ENST00000322945.11	c.34C>G	p.Pro12Ala	missense_variant	Exon 1 of 5	1	NM_002383.4	ENSP00000313362.6

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD3 exomes AF: 0.00000632 AC: 1 AN: 158228 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 91048

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000528

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000161 AC: 2 AN: 1242904 Hom.: 0 Cov.: 32 AF XY: 0.00000162 AC XY: 1 AN XY: 617456

Gnomad4 AFR exome AF: 0.0000419

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000101

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	16
DANN	Benign	0.96
DEOGEN2	Benign	0.10	T;.;.;.;.
Eigen	Benign	-0.92
Eigen_PC	Benign	-0.90
FATHMM_MKL	Benign	0.055	N
LIST_S2	Benign	0.71	T;T;T;T;T
M_CAP	Benign	0.076	D
MetaRNN	Benign	0.096	T;T;T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.0	N;N;.;.;N
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	0.51	N;N;.;D;N
REVEL	Benign	0.048
Sift	Pathogenic	0.0	D;D;.;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;T
Polyphen		0.0020	B;.;.;.;.
Vest4		0.20
MutPred		0.50		Loss of disorder (P = 0.0394);Loss of disorder (P = 0.0394);Loss of disorder (P = 0.0394);Loss of disorder (P = 0.0394);Loss of disorder (P = 0.0394);
MVP		0.20
MPC		0.013
ClinPred		0.097	T
GERP RS		-0.20
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		3.3
Varity_R		0.078
gMVP		0.075

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs530190319; hg19: chr16-29818056;