rs7858974

Positions:

• chr9-92117828-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.0763

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.153

Alfa AF: 0.142 Hom.: 2303

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7858974; hg19: chr9-94880110;