chr9-21186255-G-C

Variant names:

• chr9-21186255-G-C
• rs12236048

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 0.206 in 152,042 control chromosomes in the GnomAD database, including 3,505 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 (3505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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: 0.207 AC: 31373 AN: 151924 Hom.: 3504 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.206 AC: 31396 AN: 152042 Hom.: 3505 Cov.: 32 AF XY: 0.207 AC XY: 15406 AN XY: 74356

African (AFR) AF: 0.221 AC: 9161 AN: 41486

American (AMR) AF: 0.250 AC: 3815 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2149 AN: 5170

South Asian (SAS) AF: 0.116 AC: 559 AN: 4820

European-Finnish (FIN) AF: 0.208 AC: 2194 AN: 10570

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

European-Non Finnish (NFE) AF: 0.180 AC: 12204 AN: 67950

Other (OTH) AF: 0.200 AC: 423 AN: 2110

Alfa AF: 0.109 Hom.: 159

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.29
DANN	Benign	0.44
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs12236048; hg19: chr9-21186254;