rs3786800

Positions:

• chr19-30499793-T-C
• chr19-30499793-T-G

Variant summary

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

The NM_014717.3(ZNF536):​c.2171-35054T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,160 control chromosomes in the GnomAD database, including 2,520 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 0.17 (2520 hom., cov: 32)
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF536	NM_014717.3	c.2171-35054T>C		intron_variant		ENST00000355537.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF536	ENST00000355537.4	c.2171-35054T>C		intron_variant		1	NM_014717.3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26111 AN: 152044 Hom.: 2518 Cov.: 32

Gnomad AFR AF: 0.0963

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.172 AC: 26114 AN: 152160 Hom.: 2520 Cov.: 32 AF XY: 0.174 AC XY: 12927 AN XY: 74378

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.169

Alfa AF: 0.195 Hom.: 4408

Bravo AF: 0.167

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.029
DANN	Benign	0.33

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: rs3786800; hg19: chr19-30990700;