rs8105885

chr19-22530779-C-T

Variant summary

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

The NR_160728.1(LOC105376917):n.147+1560G>A variant causes a intron, non coding transcript 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: LOC105376917 NR_160728.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

Genes affected

LOC105376917 (HGNC:):

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376917	NR_160728.1	n.147+1560G>A		intron_variant, non_coding_transcript_variant
LOC105376917	NR_160727.1	n.147+1560G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF98	ENST00000593802.1	c.48+1560G>A		intron_variant		3
ZNF98	ENST00000599879.1	n.147+1560G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0884

Gnomad4 ASJ AF: 0.0949

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.104

Alfa AF: 0.104 Hom.: 155

Bravo AF: 0.117

Asia WGS AF: 0.321 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.7
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8105885; hg19: chr19-22713581;