9-97859836-C-G

Variant names:

• chr9-97859836-C-G
• rs874004

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 0.501 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
• Publications: 8 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.626 AC: 25936 AN: 41430

American (AMR) AF: 0.492 AC: 7522 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3468

East Asian (EAS) AF: 0.833 AC: 4303 AN: 5168

South Asian (SAS) AF: 0.599 AC: 2887 AN: 4820

European-Finnish (FIN) AF: 0.491 AC: 5179 AN: 10554

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27524 AN: 67952

Other (OTH) AF: 0.474 AC: 1000 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.73
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs874004; hg19: chr9-100622118;