chr19-22501274-T-C

Variant names:

• chr19-22501274-T-C
• rs10518257
• ENST00000593802.1:c.315+13090A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000593802.1(ZNF98):​c.315+13090A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00745 in 152,310 control chromosomes in the GnomAD database, including 12 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 0.0075 (12 hom., cov: 33)
• Consequence: ZNF98 ENST00000593802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799
• Publications: 0 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]

LOC105376917 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00745 (1135/152310) while in subpopulation EAS AF = 0.0216 (112/5180). AF 95% confidence interval is 0.0184. There are 12 homozygotes in GnomAd4. There are 560 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376917	NR_160727.1	n.414+13090A>G		intron_variant	Intron 2 of 2
LOC105376917	NR_160728.1	n.147+31065A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF98	ENST00000593802.1	c.315+13090A>G		intron_variant	Intron 2 of 2	3		ENSP00000472301.1
ZNF98	ENST00000599879.1	n.147+31065A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.00744 AC: 1132 AN: 152192 Hom.: 12 Cov.: 33

Gnomad AFR AF: 0.00900

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00635

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.00870

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00507

Gnomad OTH AF: 0.0129

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

GnomAD4 genome AF: 0.00745 AC: 1135 AN: 152310 Hom.: 12 Cov.: 33 AF XY: 0.00752 AC XY: 560 AN XY: 74480

African (AFR) AF: 0.00909 AC: 378 AN: 41570

American (AMR) AF: 0.00635 AC: 97 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3472

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5180

South Asian (SAS) AF: 0.00829 AC: 40 AN: 4826

European-Finnish (FIN) AF: 0.00160 AC: 17 AN: 10626

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00507 AC: 345 AN: 68032

Other (OTH) AF: 0.0132 AC: 28 AN: 2114

Alfa AF: 0.00726 Hom.: 2

Bravo AF: 0.00832

Asia WGS AF: 0.0180 AC: 64 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	13
DANN	Benign	0.77
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs10518257; hg19: chr19-22684076;