9-21193433-T-A

Variant names:

• chr9-21193433-T-A
• rs10811497

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 0.208 in 151,882 control chromosomes in the GnomAD database, including 3,616 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 0.21 (3616 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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: 0.208 AC: 31603 AN: 151764 Hom.: 3613 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.208 AC: 31644 AN: 151882 Hom.: 3616 Cov.: 31 AF XY: 0.209 AC XY: 15492 AN XY: 74232

African (AFR) AF: 0.246 AC: 10207 AN: 41418

American (AMR) AF: 0.250 AC: 3811 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 688 AN: 3464

East Asian (EAS) AF: 0.413 AC: 2113 AN: 5116

South Asian (SAS) AF: 0.113 AC: 543 AN: 4810

European-Finnish (FIN) AF: 0.197 AC: 2084 AN: 10568

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11593 AN: 67938

Other (OTH) AF: 0.201 AC: 423 AN: 2102

Alfa AF: 0.108 Hom.: 162

Bravo AF: 0.217

Asia WGS AF: 0.251 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.096
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10811497; hg19: chr9-21193432; COSMIC: COSV71625218;