19-30353182-C-T

Position:

• chr19-30353182-C-T

Variant summary

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

The NM_001376110.1(ZNF536):​c.-3+69041C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,974 control chromosomes in the GnomAD database, including 7,183 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 0.31 (7183 hom., cov: 32)
• Consequence: ZNF536 NM_001376110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

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]

ZNF536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF536	NM_001376110.1	c.-3+69041C>T		intron_variant			NP_001363039.1
ZNF536	NM_001376111.1	c.-3+69041C>T		intron_variant			NP_001363040.1
ZNF536	XM_011527554.3	c.-3+698C>T		intron_variant			XP_011525856.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF536	ENST00000592773.3	c.-3+69041C>T		intron_variant		5		ENSP00000467909.3
ZNF536	ENST00000706148.1	c.-3+69041C>T		intron_variant				ENSP00000516231.1
ZNF536	ENST00000706142.1	c.-3+698C>T		intron_variant				ENSP00000516226.1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46582 AN: 151856 Hom.: 7192 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.307 AC: 46587 AN: 151974 Hom.: 7183 Cov.: 32 AF XY: 0.301 AC XY: 22385 AN XY: 74272

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.330

Alfa AF: 0.326 Hom.: 14376

Bravo AF: 0.315

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11673050; hg19: chr19-30844089;