rs953294

Variant names:

• chr9-103605368-G-A
• rs953294

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.221 AC: 9161 AN: 41394

American (AMR) AF: 0.126 AC: 1912 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 820 AN: 3462

East Asian (EAS) AF: 0.174 AC: 899 AN: 5156

South Asian (SAS) AF: 0.197 AC: 947 AN: 4816

European-Finnish (FIN) AF: 0.0875 AC: 921 AN: 10522

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10106 AN: 67908

Other (OTH) AF: 0.168 AC: 355 AN: 2108

Alfa AF: 0.162 Hom.: 739

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
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs953294; hg19: chr9-106367650;