17-5254520-A-G

Variant names:

• chr17-5254520-A-G
• rs4356530
• ENST00000780152.1:n.459-409A>G

Variant summary

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

The ENST00000780152.1(ZNF594-DT):​n.459-409A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 152,108 control chromosomes in the GnomAD database, including 70,525 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 0.96 (70525 hom., cov: 30)
• Consequence: ZNF594-DT ENST00000780152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 6 publications found

Genes affected

ZNF594-DT (HGNC:55347): (ZNF594 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780152.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF594-DT	ENST00000780152.1		n.459-409A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146128 AN: 151990 Hom.: 70490 Cov.: 30

Gnomad AFR AF: 0.869

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.961 AC: 146220 AN: 152108 Hom.: 70525 Cov.: 30 AF XY: 0.962 AC XY: 71531 AN XY: 74348

African (AFR) AF: 0.869 AC: 36002 AN: 41438

American (AMR) AF: 0.981 AC: 14975 AN: 15264

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3470 AN: 3470

East Asian (EAS) AF: 0.990 AC: 5117 AN: 5168

South Asian (SAS) AF: 0.998 AC: 4816 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10592 AN: 10592

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67988 AN: 68034

Other (OTH) AF: 0.973 AC: 2056 AN: 2112

Alfa AF: 0.972 Hom.: 9320

Bravo AF: 0.955

Asia WGS AF: 0.989 AC: 3439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4356530; hg19: chr17-5157815;