rs931608

Positions:

• chr19-22431320-A-C
• chr19-22431320-A-G
• chr19-22431320-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000593802.1(ZNF98):​c.316-27808T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 151,942 control chromosomes in the GnomAD database, including 55,606 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 0.85 (55606 hom., cov: 31)
• Consequence: ZNF98 ENST00000593802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF98	ENST00000593802.1	c.316-27808T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129728 AN: 151824 Hom.: 55575 Cov.: 31

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.854 AC: 129813 AN: 151942 Hom.: 55606 Cov.: 31 AF XY: 0.852 AC XY: 63239 AN XY: 74222

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.867

Alfa AF: 0.873 Hom.: 78244

Bravo AF: 0.851

Asia WGS AF: 0.865 AC: 3009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs931608; hg19: chr19-22614122;