19-30353182-C-T

Variant names:

• chr19-30353182-C-T
• rs11673050
• NM_001376110.1:c.-3+69041C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001376110.1. 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
	ZNF536	NM_001376110.1		c.-3+69041C>T		intron	N/A	NP_001363039.1	K7EQN6
	ZNF536	NM_001376111.1		c.-3+69041C>T		intron	N/A	NP_001363040.1	K7EQN6
	ZNF536	NM_001438953.1		c.-3+69041C>T		intron	N/A	NP_001425882.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF536	ENST00000592773.3	TSL:5	c.-3+69041C>T		intron	N/A	ENSP00000467909.3	K7EQN6
	ZNF536	ENST00000706148.1		c.-3+69041C>T		intron	N/A	ENSP00000516231.1	A0A994J7Z0
	ZNF536	ENST00000706142.1		c.-3+698C>T		intron	N/A	ENSP00000516226.1	O15090

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

African (AFR) AF: 0.307 AC: 12704 AN: 41420

American (AMR) AF: 0.311 AC: 4746 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1236 AN: 5156

South Asian (SAS) AF: 0.339 AC: 1634 AN: 4816

European-Finnish (FIN) AF: 0.223 AC: 2360 AN: 10566

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21633 AN: 67972

Other (OTH) AF: 0.330 AC: 696 AN: 2112

Alfa AF: 0.321 Hom.: 31977

Bravo AF: 0.315

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.5
DANN	Benign	0.72
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs11673050; hg19: chr19-30844089;