rs320209

Positions:

• chr9-102182473-A-T

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 0.0768 in 152,154 control chromosomes in the GnomAD database, including 603 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 0.077 (603 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.14 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: 0.0768 AC: 11676 AN: 152036 Hom.: 601 Cov.: 32

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0589

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0693

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

GnomAD4 genome AF: 0.0768 AC: 11680 AN: 152154 Hom.: 603 Cov.: 32 AF XY: 0.0759 AC XY: 5646 AN XY: 74360

Gnomad4 AFR AF: 0.0189

Gnomad4 AMR AF: 0.0869

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0589

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0686

Alfa AF: 0.0962 Hom.: 370

Bravo AF: 0.0749

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs320209; hg19: chr9-104944755;