9-21217536-C-G

Position:

• chr9-21217536-C-G

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 0.194 in 151,992 control chromosomes in the GnomAD database, including 3,127 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 (3127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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: 0.194 AC: 29511 AN: 151874 Hom.: 3124 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.194 AC: 29538 AN: 151992 Hom.: 3127 Cov.: 32 AF XY: 0.195 AC XY: 14492 AN XY: 74286

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.193

Alfa AF: 0.0919 Hom.: 139

Bravo AF: 0.201

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.064
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: rs1834247; hg19: chr9-21217535;