rs1689965

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-5181468-G-A
• chr17-5181468-G-C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The NM_032530.2(ZNF594):​c.*365C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.982 in 152,284 control chromosomes in the GnomAD database, including 73,460 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 0.98 (73460 hom., cov: 31)
  • Exomes 𝑓: 1.0 (727689 hom.)
  • Failed GnomAD Quality Control
• 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: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.229).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

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>T		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>T		3_prime_UTR	Exon 2 of 2	ENSP00000461032.1
	ZNF594	ENST00000399604.4	TSL:6	c.*365C>T		3_prime_UTR	Exon 1 of 1	ENSP00000382513.4

Frequencies

GnomAD3 genomes AF: 0.982 AC: 149391 AN: 152166 Hom.: 73407 Cov.: 31

Gnomad AFR AF: 0.939

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.990

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.999

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.987

GnomAD2 exomes AF: 0.995 AC: 248866 AN: 250214 AF XY: 0.996

Gnomad AFR exome AF: 0.933

Gnomad AMR exome AF: 0.993

Gnomad ASJ exome AF: 0.999

Gnomad EAS exome AF: 1.00

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 1.00

Gnomad OTH exome AF: 0.998

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.998 AC: 1458495 AN: 1461756 Hom.: 727689 Cov.: 74 AF XY: 0.998 AC XY: 725754 AN XY: 727192

African (AFR) AF: 0.940 AC: 31458 AN: 33480

American (AMR) AF: 0.993 AC: 44424 AN: 44722

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 26122 AN: 26130

East Asian (EAS) AF: 0.998 AC: 39624 AN: 39700

South Asian (SAS) AF: 1.00 AC: 86253 AN: 86254

European-Finnish (FIN) AF: 1.00 AC: 53420 AN: 53420

Middle Eastern (MID) AF: 0.997 AC: 5748 AN: 5768

European-Non Finnish (NFE) AF: 1.00 AC: 1111344 AN: 1111892

Other (OTH) AF: 0.995 AC: 60102 AN: 60390

GnomAD4 genome AF: 0.982 AC: 149501 AN: 152284 Hom.: 73460 Cov.: 31 AF XY: 0.983 AC XY: 73151 AN XY: 74452

African (AFR) AF: 0.939 AC: 39000 AN: 41534

American (AMR) AF: 0.990 AC: 15144 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3470 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5171 AN: 5174

South Asian (SAS) AF: 1.00 AC: 4822 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10616 AN: 10616

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67987 AN: 68038

Other (OTH) AF: 0.987 AC: 2089 AN: 2116

Alfa AF: 0.993 Hom.: 13205

Bravo AF: 0.979

Asia WGS AF: 0.998 AC: 3470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.9
DANN	Benign	0.76
PhyloP100		0.31
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: rs1689965; hg19: chr17-5084763;