rs33428

chr19-30446936-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014717.3(ZNF536):c.2170+1204A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,126 control chromosomes in the GnomAD database, including 38,611 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (38611 hom., cov: 33)
• Consequence: ZNF536 NM_014717.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

ZNF536 (HGNC:29025): (zinc finger protein 536) The protein encoded by this gene is a highly conserved zinc finger protein. The encoded protein is most abundant in brain, where it negatively regulates neuronal differentiation. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF536	NM_014717.3	c.2170+1204A>G		intron_variant		ENST00000355537.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF536	ENST00000355537.4	c.2170+1204A>G		intron_variant		1	NM_014717.3

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107113 AN: 152008 Hom.: 38562 Cov.: 33

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.705

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.705 AC: 107228 AN: 152126 Hom.: 38611 Cov.: 33 AF XY: 0.694 AC XY: 51605 AN XY: 74368

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.702

Alfa AF: 0.696 Hom.: 37010

Bravo AF: 0.705

Asia WGS AF: 0.436 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	12
Dann	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs33428; hg19: chr19-30937843;