17-5181468-G-C

Variant names:

• chr17-5181468-G-C
• rs1689965
• NM_032530.2:c.*365C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032530.2(ZNF594):​c.*365C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: ZNF594 NM_032530.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 7 publications found

Genes affected

ZNF594 (HGNC:29392): (zinc finger protein 594) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.128).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032530.2. 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
	ZNF594	NM_032530.2	MANE Select	c.*365C>G		3_prime_UTR	Exon 2 of 2	NP_115919.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF594	ENST00000575779.2	TSL:3 MANE Select	c.*365C>G		3_prime_UTR	Exon 2 of 2	ENSP00000461032.1
	ZNF594	ENST00000399604.4	TSL:6	c.*365C>G		3_prime_UTR	Exon 1 of 1	ENSP00000382513.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 74

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 13205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		0.31

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: rs1689965; hg19: chr17-5084763;