chr9-21188208-C-T

Variant names:

• chr9-21188208-C-T
• rs10964896

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 0.201 in 152,074 control chromosomes in the GnomAD database, including 3,371 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 (3371 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30588 AN: 151956 Hom.: 3370 Cov.: 33

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.201 AC: 30611 AN: 152074 Hom.: 3371 Cov.: 33 AF XY: 0.202 AC XY: 15014 AN XY: 74344

African (AFR) AF: 0.220 AC: 9132 AN: 41476

American (AMR) AF: 0.248 AC: 3794 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2144 AN: 5176

South Asian (SAS) AF: 0.112 AC: 543 AN: 4828

European-Finnish (FIN) AF: 0.199 AC: 2103 AN: 10582

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

European-Non Finnish (NFE) AF: 0.171 AC: 11601 AN: 67944

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.195 Hom.: 378

Bravo AF: 0.208

Asia WGS AF: 0.246 AC: 857 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.27
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10964896; hg19: chr9-21188207;