rs10964932

Variant names:

• chr9-21241857-T-A
• rs10964932

Your query was ambiguous. Multiple possible variants found:

• chr9-21241857-T-A
• chr9-21241857-T-G

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 0.209 in 151,608 control chromosomes in the GnomAD database, including 3,597 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 (3597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 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: 0.209 AC: 31609 AN: 151490 Hom.: 3594 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.209 AC: 31644 AN: 151608 Hom.: 3597 Cov.: 32 AF XY: 0.210 AC XY: 15530 AN XY: 74066

African (AFR) AF: 0.252 AC: 10425 AN: 41324

American (AMR) AF: 0.252 AC: 3838 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 694 AN: 3458

East Asian (EAS) AF: 0.399 AC: 2055 AN: 5146

South Asian (SAS) AF: 0.113 AC: 543 AN: 4792

European-Finnish (FIN) AF: 0.192 AC: 2017 AN: 10498

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11462 AN: 67854

Other (OTH) AF: 0.204 AC: 430 AN: 2104

Alfa AF: 0.105 Hom.: 154

Bravo AF: 0.217

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10964932; hg19: chr9-21241856;