rs953294

Positions:

• chr9-103605368-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;