rs931608

Variant names:

• chr19-22431320-A-C
• rs931608
• ENST00000593802.1:c.316-27808T>G

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF98	ENST00000593802.1	c.316-27808T>G		intron_variant	Intron 2 of 2	3		ENSP00000472301.1

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;