ENST00000593802.1:c.48+1560G>A

Variant names:

• chr19-22530779-C-T
• rs8105885
• ENST00000593802.1:c.48+1560G>A

Variant summary

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

The ENST00000593802.1(ZNF98):​c.48+1560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,900 control chromosomes in the GnomAD database, including 1,384 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 0.12 (1384 hom., cov: 32)
• Consequence: ZNF98 ENST00000593802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 4 publications found

Genes affected

ZNF98 (HGNC:13174): (zinc finger protein 98) Predicted to enable DNA-binding transcription factor 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, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

LOC105376917 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593802.1. 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
	LOC105376917	NR_160727.1		n.147+1560G>A		intron	N/A
	LOC105376917	NR_160728.1		n.147+1560G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF98	ENST00000593802.1	TSL:3	c.48+1560G>A		intron	N/A	ENSP00000472301.1
	ZNF98	ENST00000599879.1	TSL:3	n.147+1560G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18202 AN: 151784 Hom.: 1377 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.0949

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.120 AC: 18226 AN: 151900 Hom.: 1384 Cov.: 32 AF XY: 0.126 AC XY: 9350 AN XY: 74206

African (AFR) AF: 0.145 AC: 5987 AN: 41422

American (AMR) AF: 0.0884 AC: 1348 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0949 AC: 329 AN: 3466

East Asian (EAS) AF: 0.365 AC: 1877 AN: 5146

South Asian (SAS) AF: 0.270 AC: 1299 AN: 4804

European-Finnish (FIN) AF: 0.126 AC: 1330 AN: 10530

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0846 AC: 5748 AN: 67970

Other (OTH) AF: 0.104 AC: 219 AN: 2108

Alfa AF: 0.105 Hom.: 166

Bravo AF: 0.117

Asia WGS AF: 0.321 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.7
DANN	Benign	0.47
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs8105885; hg19: chr19-22713581;