chr9-87709285-G-A

Position:

• chr9-87709285-G-A

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 0.401 in 152,018 control chromosomes in the GnomAD database, including 13,477 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 0.40 (13477 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.483 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: 0.401 AC: 60916 AN: 151900 Hom.: 13488 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.401 AC: 60905 AN: 152018 Hom.: 13477 Cov.: 32 AF XY: 0.406 AC XY: 30146 AN XY: 74292

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.423

Alfa AF: 0.471 Hom.: 23098

Bravo AF: 0.396

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118866; hg19: chr9-90324200;