rs953294

Variant names:

• chr9-103605368-G-A
• rs953294

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 0.167 in 151,800 control chromosomes in the GnomAD database, including 2,275 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 0.17 (2275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25225 AN: 151682 Hom.: 2266 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.167 AC: 25280 AN: 151800 Hom.: 2275 Cov.: 32 AF XY: 0.165 AC XY: 12259 AN XY: 74150

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.0875

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.168

Alfa AF: 0.162 Hom.: 402

Bravo AF: 0.168

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs953294; hg19: chr9-106367650;