chr19-22425572-T-C

Variant names:

• chr19-22425572-T-C
• rs10404998
• ENST00000593802.1:c.316-22060A>G

Variant summary

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

The ENST00000593802.1(ZNF98):​c.316-22060A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,884 control chromosomes in the GnomAD database, including 14,092 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 0.43 (14092 hom., cov: 32)
• Consequence: ZNF98 ENST00000593802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 11 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]

ENSG00000269796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF98	ENST00000593802.1	c.316-22060A>G		intron_variant	Intron 2 of 2	3		ENSP00000472301.1
ENSG00000269796	ENST00000599129.1	n.40-333T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64862 AN: 151766 Hom.: 14089 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.427 AC: 64891 AN: 151884 Hom.: 14092 Cov.: 32 AF XY: 0.420 AC XY: 31181 AN XY: 74222

African (AFR) AF: 0.426 AC: 17648 AN: 41438

American (AMR) AF: 0.363 AC: 5531 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1077 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1889 AN: 5136

South Asian (SAS) AF: 0.275 AC: 1322 AN: 4808

European-Finnish (FIN) AF: 0.441 AC: 4655 AN: 10548

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.461 AC: 31330 AN: 67926

Other (OTH) AF: 0.400 AC: 843 AN: 2108

Alfa AF: 0.438 Hom.: 20786

Bravo AF: 0.427

Asia WGS AF: 0.288 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.5
DANN	Benign	0.60
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10404998; hg19: chr19-22608374;