rs7858974

Variant names:

• chr9-92117828-A-G
• rs7858974

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.166 in 152,152 control chromosomes in the GnomAD database, including 2,446 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 0.17 (2446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.919
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25153 AN: 152032 Hom.: 2441 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.166 AC: 25182 AN: 152152 Hom.: 2446 Cov.: 32 AF XY: 0.162 AC XY: 12047 AN XY: 74392

African (AFR) AF: 0.266 AC: 11023 AN: 41478

American (AMR) AF: 0.119 AC: 1817 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3470

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5182

South Asian (SAS) AF: 0.0763 AC: 368 AN: 4824

European-Finnish (FIN) AF: 0.142 AC: 1507 AN: 10596

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9060 AN: 67996

Other (OTH) AF: 0.153 AC: 322 AN: 2108

Alfa AF: 0.145 Hom.: 3356

Bravo AF: 0.168

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.70
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs7858974; hg19: chr9-94880110;