chr9-21086341-A-G

Position:

• chr9-21086341-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 0.118 in 151,850 control chromosomes in the GnomAD database, including 1,146 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 0.12 (1146 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 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: 0.118 AC: 17916 AN: 151732 Hom.: 1144 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0540

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.118 AC: 17922 AN: 151850 Hom.: 1146 Cov.: 31 AF XY: 0.117 AC XY: 8653 AN XY: 74204

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0829

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0540

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0551 Hom.: 59

Bravo AF: 0.121

Asia WGS AF: 0.195 AC: 675 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10811469; hg19: chr9-21086340; COSMIC: COSV69450610;