chr15-84787514-C-T

Variant names:

• chr15-84787514-C-T
• rs10438428
• NM_014630.3:c.2220+2619C>T

Variant summary

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

The NM_014630.3(ZNF592):​c.2220+2619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,964 control chromosomes in the GnomAD database, including 25,722 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 0.57 (25722 hom., cov: 31)
• Consequence: ZNF592 NM_014630.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 17 publications found

Genes affected

ZNF592 (HGNC:28986): (zinc finger protein 592) This gene is thought to play a role in a complex developmental pathway and the regulation of genes involved in cerebellar development. Mutations in this gene have been associated with autosomal recessive spinocerebellar ataxia. [provided by RefSeq, Jan 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014630.3. 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
	ZNF592	NM_014630.3	MANE Select	c.2220+2619C>T		intron	N/A	NP_055445.2	Q92610

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF592	ENST00000560079.7	TSL:1 MANE Select	c.2220+2619C>T		intron	N/A	ENSP00000452877.2	Q92610
	ZNF592	ENST00000559607.1	TSL:1	n.2220+2619C>T		intron	N/A	ENSP00000453491.1	H0YM74
	ZNF592	ENST00000877254.1		c.2220+2619C>T		intron	N/A	ENSP00000547313.1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85978 AN: 151846 Hom.: 25678 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.566 AC: 86078 AN: 151964 Hom.: 25722 Cov.: 31 AF XY: 0.567 AC XY: 42115 AN XY: 74246

African (AFR) AF: 0.762 AC: 31597 AN: 41476

American (AMR) AF: 0.534 AC: 8156 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4098 AN: 5150

South Asian (SAS) AF: 0.541 AC: 2599 AN: 4808

European-Finnish (FIN) AF: 0.456 AC: 4809 AN: 10546

Middle Eastern (MID) AF: 0.397 AC: 115 AN: 290

European-Non Finnish (NFE) AF: 0.466 AC: 31635 AN: 67930

Other (OTH) AF: 0.527 AC: 1110 AN: 2108

Alfa AF: 0.485 Hom.: 30721

Bravo AF: 0.579

Asia WGS AF: 0.673 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.38
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10438428; hg19: chr15-85330745;