ENST00000219782.11:c.1464G>C

Variant names:

• chr16-29809724-G-C
• ENST00000219782.11:c.1464G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000219782.11(MAZ):​c.1464G>C​(p.Gln488His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MAZ ENST00000219782.11 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.273
• Publications: 0 publications found

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)

ENSG00000280607 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13465273).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000219782.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAZ	NM_002383.4	MANE Select	c.1280-353G>C		intron	N/A	NP_002374.2	P56270-1
	MAZ	NM_001042539.3		c.1464G>C	p.Gln488His	missense	Exon 5 of 6	NP_001036004.1	P56270-2
	MAZ	NM_001276275.2		c.1211-353G>C		intron	N/A	NP_001263204.1	P56270-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAZ	ENST00000219782.11	TSL:1	c.1464G>C	p.Gln488His	missense	Exon 5 of 6	ENSP00000219782.6	P56270-2
	MAZ	ENST00000322945.11	TSL:1 MANE Select	c.1280-353G>C		intron	N/A	ENSP00000313362.6	P56270-1
	MAZ	ENST00000545521.5	TSL:1	c.1211-353G>C		intron	N/A	ENSP00000443956.1	P56270-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	21
DANN	Benign	0.90
Eigen	Benign	-0.52
Eigen_PC	Benign	-0.37
FATHMM_MKL	Benign	0.67	D
LIST_S2	Benign	0.53	T
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.13	T
MetaSVM	Benign	-0.96	T
PhyloP100		0.27
PrimateAI	Uncertain	0.78	T
PROVEAN	Benign	-0.19	N
REVEL	Benign	0.054
Sift	Uncertain	0.0090	D
Sift4G	Uncertain	0.027	D
Vest4		0.39
MutPred		0.33		Loss of glycosylation at P491 (P = 0.1249)
MVP		0.23
MPC		0.91
ClinPred		0.51	D
GERP RS		3.1
gMVP		0.22

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

hg19: chr16-29821045;