rs1216119

chr19-22527043-C-A

Variant summary

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

The NR_110427.1(LOC101929124):n.907G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,078 control chromosomes in the GnomAD database, including 7,270 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 0.30 (7268 hom., cov: 32)
  • Exomes 𝑓: 0.35 (2 hom.)
• Consequence: LOC101929124 NR_110427.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

(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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929124	NR_110427.1	n.907G>T		non_coding_transcript_exon_variant	1/5
LOC105376917	NR_160728.1	n.147+5296G>T		intron_variant, non_coding_transcript_variant
LOC105376917	NR_160727.1	n.147+5296G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000562262.1	n.907G>T		non_coding_transcript_exon_variant	1/5	2
ZNF98	ENST00000593802.1	c.48+5296G>T		intron_variant		3
ZNF98	ENST00000599879.1	n.147+5296G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45054 AN: 151920 Hom.: 7261 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.308

GnomAD4 exome AF: 0.350 AC: 14 AN: 40 Hom.: 2 Cov.: 0 AF XY: 0.429 AC XY: 12 AN XY: 28

Gnomad4 AFR exome AF: 0.375

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.321

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.297 AC: 45100 AN: 152038 Hom.: 7268 Cov.: 32 AF XY: 0.305 AC XY: 22630 AN XY: 74302

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.307

Alfa AF: 0.293 Hom.: 3833

Bravo AF: 0.297

Asia WGS AF: 0.551 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	6.5
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1216119; hg19: chr19-22709845;