chr9-21216029-C-T

Variant names:

• chr9-21216029-C-T
• rs10125010

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 0.287 in 151,828 control chromosomes in the GnomAD database, including 6,957 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 0.29 (6957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 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: 0.286 AC: 43422 AN: 151712 Hom.: 6933 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.287 AC: 43506 AN: 151828 Hom.: 6957 Cov.: 32 AF XY: 0.286 AC XY: 21201 AN XY: 74204

African (AFR) AF: 0.403 AC: 16669 AN: 41366

American (AMR) AF: 0.313 AC: 4758 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3466

East Asian (EAS) AF: 0.514 AC: 2653 AN: 5162

South Asian (SAS) AF: 0.195 AC: 938 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2200 AN: 10526

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14655 AN: 67950

Other (OTH) AF: 0.272 AC: 573 AN: 2110

Alfa AF: 0.248 Hom.: 1715

Bravo AF: 0.303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.030
DANN	Benign	0.14
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs10125010; hg19: chr9-21216028;