4-86078-G-GA

Position:

• chr4-86078-G-GA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_182524.4(ZNF595):​c.574_575insA​(p.Gly192GlufsTer12) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZNF595 NM_182524.4 frameshift
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.0680

Genes affected

ZNF595 (HGNC:27196): (zinc finger protein 595) This gene encodes a protein belonging to the Cys2His2 zinc finger protein family, whose members function as transcription factors that can regulate a broad variety of developmental and cellular processes. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Oct 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF595	NM_182524.4	c.574_575insA	p.Gly192GlufsTer12	frameshift_variant	4/4	ENST00000610261.6	NP_872330.1
ZNF595	NM_001286052.2	c.478_479insA	p.Gly160GlufsTer12	frameshift_variant	3/3		NP_001272981.1
ZNF595	NM_001286053.2	c.25_26insA	p.Gly9GlufsTer12	frameshift_variant	2/2		NP_001272982.1
ZNF595	NM_001286054.2	c.25_26insA	p.Gly9GlufsTer12	frameshift_variant	5/5		NP_001272983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF595	ENST00000610261.6	c.574_575insA	p.Gly192GlufsTer12	frameshift_variant	4/4	1	NM_182524.4	ENSP00000477392	P1
ZNF595	ENST00000608255.2	c.25_26insA	p.Gly9GlufsTer12	frameshift_variant	2/2	2		ENSP00000476367
ZNF595	ENST00000609518.5	c.478_479insA	p.Gly160GlufsTer12	frameshift_variant	3/3	2		ENSP00000476408

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1553801178; hg19: chr4-85969; COSMIC: COSV59553620;