9-21186255-G-C

Position:

• chr9-21186255-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.200

Alfa AF: 0.109 Hom.: 159

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12236048; hg19: chr9-21186254;