rs75652600

chr15-84768060-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_014630.3(ZNF592):c.-150+3245A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00513 in 99,646 control chromosomes in the GnomAD database, including 2 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 0.0051 (2 hom., cov: 23)
• Consequence: ZNF592 NM_014630.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS2: High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF592	NM_014630.3	c.-150+3245A>T		intron_variant		ENST00000560079.7
ZNF592	XM_005254996.4	c.-20+3245A>T		intron_variant
ZNF592	XM_011522246.3	c.-150+3245A>T		intron_variant
ZNF592	XM_011522247.3	c.-20+3245A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF592	ENST00000560079.7	c.-150+3245A>T		intron_variant		1	NM_014630.3	P1

Frequencies

GnomAD3 genomes AF: 0.00514 AC: 511 AN: 99506 Hom.: 2 Cov.: 23

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00213

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000253

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000694

Gnomad MID AF: 0.00694

Gnomad NFE AF: 0.000635

Gnomad OTH AF: 0.00564

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

GnomAD4 genome AF: 0.00513 AC: 511 AN: 99646 Hom.: 2 Cov.: 23 AF XY: 0.00475 AC XY: 232 AN XY: 48812

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.00213

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000253

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000694

Gnomad4 NFE AF: 0.000636

Gnomad4 OTH AF: 0.00553

Alfa AF: 0.198 Hom.: 115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.81
Dann	Benign	0.15

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

Publications

LitVar

Other links and lift over

dbSNP: rs75652600; hg19: chr15-85311291;