rs16964420

Variant names:

• chr19-30619326-G-A
• rs16964420
• NM_001376110.1:c.3895+69812G>A

Variant summary

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

The NM_001376110.1(ZNF536):​c.3895+69812G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,906 control chromosomes in the GnomAD database, including 8,655 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 0.33 (8655 hom., cov: 32)
• Consequence: ZNF536 NM_001376110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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.3895+69812G>A		intron	N/A	NP_001363039.1	K7EQN6
	ZNF536	NM_001376111.1		c.3895+69812G>A		intron	N/A	NP_001363040.1	K7EQN6
	ZNF536	NM_001438953.1		c.3895+69812G>A		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.3895+69812G>A		intron	N/A	ENSP00000467909.3	K7EQN6
	ZNF536	ENST00000706148.1		c.3896-24211G>A		intron	N/A	ENSP00000516231.1	A0A994J7Z0
	ZNF536	ENST00000706150.1		c.3896-24211G>A		intron	N/A	ENSP00000516233.1	A0A994J7Z0

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49557 AN: 151786 Hom.: 8645 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.326 AC: 49588 AN: 151906 Hom.: 8655 Cov.: 32 AF XY: 0.333 AC XY: 24701 AN XY: 74186

African (AFR) AF: 0.223 AC: 9244 AN: 41422

American (AMR) AF: 0.406 AC: 6204 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2494 AN: 5158

South Asian (SAS) AF: 0.398 AC: 1914 AN: 4810

European-Finnish (FIN) AF: 0.467 AC: 4913 AN: 10528

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.333 AC: 22632 AN: 67952

Other (OTH) AF: 0.330 AC: 694 AN: 2102

Alfa AF: 0.332 Hom.: 15874

Bravo AF: 0.316

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.53
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs16964420; hg19: chr19-31110233;