19-30646729-T-G

Variant names:

• chr19-30646729-T-G
• rs892095
• NM_001376110.1:c.3896-64028T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001376110.1(ZNF536):​c.3896-64028T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,256 control chromosomes in the GnomAD database, including 68,988 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 0.95 (68988 hom., cov: 32)
• Consequence: ZNF536 NM_001376110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF536	NM_001376110.1		c.3896-64028T>G		intron	N/A	NP_001363039.1
	ZNF536	NM_001376111.1		c.3896-64028T>G		intron	N/A	NP_001363040.1
	ZNF536	NM_001438953.1		c.3896-64028T>G		intron	N/A	NP_001425882.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF536	ENST00000592773.3	TSL:5	c.3896-64028T>G		intron	N/A	ENSP00000467909.3
	ZNF536	ENST00000706148.1		c.*26+3153T>G		intron	N/A	ENSP00000516231.1
	ZNF536	ENST00000706150.1		c.*26+3153T>G		intron	N/A	ENSP00000516233.1

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144584 AN: 152138 Hom.: 68955 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.950 AC: 144670 AN: 152256 Hom.: 68988 Cov.: 32 AF XY: 0.950 AC XY: 70770 AN XY: 74460

African (AFR) AF: 0.870 AC: 36115 AN: 41512

American (AMR) AF: 0.903 AC: 13817 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3435 AN: 3472

East Asian (EAS) AF: 0.989 AC: 5124 AN: 5182

South Asian (SAS) AF: 0.976 AC: 4707 AN: 4822

European-Finnish (FIN) AF: 0.999 AC: 10608 AN: 10614

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67664 AN: 68040

Other (OTH) AF: 0.953 AC: 2014 AN: 2114

Alfa AF: 0.970 Hom.: 8899

Bravo AF: 0.939

Asia WGS AF: 0.967 AC: 3363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.019
DANN	Benign	0.31
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs892095; hg19: chr19-31137636;