9-21188353-T-C

Variant names:

• chr9-21188353-T-C
• rs10964899

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 0.224 in 152,110 control chromosomes in the GnomAD database, including 4,258 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 0.22 (4258 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33972 AN: 151992 Hom.: 4246 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.224 AC: 34036 AN: 152110 Hom.: 4258 Cov.: 33 AF XY: 0.224 AC XY: 16686 AN XY: 74354

African (AFR) AF: 0.298 AC: 12348 AN: 41502

American (AMR) AF: 0.258 AC: 3937 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2133 AN: 5164

South Asian (SAS) AF: 0.112 AC: 543 AN: 4830

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10566

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11653 AN: 67976

Other (OTH) AF: 0.216 AC: 455 AN: 2110

Alfa AF: 0.210 Hom.: 458

Bravo AF: 0.234

Asia WGS AF: 0.256 AC: 892 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.83
DANN	Benign	0.60
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs10964899; hg19: chr9-21188352;