chr9-21229328-A-C

Position:

• chr9-21229328-A-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 0.237 in 152,044 control chromosomes in the GnomAD database, including 4,970 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 0.24 (4970 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36057 AN: 151924 Hom.: 4964 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.237 AC: 36093 AN: 152044 Hom.: 4970 Cov.: 33 AF XY: 0.239 AC XY: 17746 AN XY: 74324

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.221

Alfa AF: 0.0963 Hom.: 139

Bravo AF: 0.249

Asia WGS AF: 0.329 AC: 1139 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1831391; hg19: chr9-21229327;