9-21203009-A-T

Variant names:

• chr9-21203009-A-T
• rs10811502

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 0.203 in 151,942 control chromosomes in the GnomAD database, including 3,461 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 0.20 (3461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30804 AN: 151824 Hom.: 3460 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.203 AC: 30826 AN: 151942 Hom.: 3461 Cov.: 32 AF XY: 0.203 AC XY: 15085 AN XY: 74264

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.198

Alfa AF: 0.194 Hom.: 359

Bravo AF: 0.210

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10811502; hg19: chr9-21203008;