9-108799186-G-A

Position:

• chr9-108799186-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 0.0913 in 152,108 control chromosomes in the GnomAD database, including 852 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 0.091 (852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

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 (NFE) allele frequency at 95% confidence interval = 0.118 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: 0.0914 AC: 13888 AN: 151990 Hom.: 853 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0913 AC: 13882 AN: 152108 Hom.: 852 Cov.: 32 AF XY: 0.0951 AC XY: 7067 AN XY: 74350

Gnomad4 AFR AF: 0.0234

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.0980

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0939

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.103 Hom.: 147

Bravo AF: 0.0806

Asia WGS AF: 0.130 AC: 450 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	4.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10979500; hg19: chr9-111561466;