9-21153986-A-G

Variant names:

• chr9-21153986-A-G
• rs10811482

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 0.194 in 152,014 control chromosomes in the GnomAD database, including 3,187 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 0.19 (3187 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29439 AN: 151896 Hom.: 3189 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.194 AC: 29443 AN: 152014 Hom.: 3187 Cov.: 31 AF XY: 0.193 AC XY: 14342 AN XY: 74270

African (AFR) AF: 0.125 AC: 5191 AN: 41472

American (AMR) AF: 0.140 AC: 2135 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5172

South Asian (SAS) AF: 0.215 AC: 1033 AN: 4812

European-Finnish (FIN) AF: 0.275 AC: 2897 AN: 10530

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16844 AN: 67966

Other (OTH) AF: 0.192 AC: 406 AN: 2110

Alfa AF: 0.221 Hom.: 6517

Bravo AF: 0.177

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.98
DANN	Benign	0.57
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10811482; hg19: chr9-21153985;