9-97859836-C-G

Position:

• chr9-97859836-C-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 0.501 in 151,988 control chromosomes in the GnomAD database, including 20,158 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 0.50 (20158 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76116 AN: 151870 Hom.: 20124 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.501 AC: 76187 AN: 151988 Hom.: 20158 Cov.: 31 AF XY: 0.510 AC XY: 37842 AN XY: 74264

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.474

Alfa AF: 0.302 Hom.: 745

Bravo AF: 0.506

Asia WGS AF: 0.669 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs874004; hg19: chr9-100622118;