rs9293474

Variant names:

• chr5-86672317-G-A
• rs9293474

Your query was ambiguous. Multiple possible variants found:

• chr5-86672317-G-A
• chr5-86672317-G-C

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 0.87 in 152,044 control chromosomes in the GnomAD database, including 58,382 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 0.87 (58382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132156 AN: 151926 Hom.: 58342 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.870 AC: 132251 AN: 152044 Hom.: 58382 Cov.: 32 AF XY: 0.871 AC XY: 64705 AN XY: 74318

African (AFR) AF: 0.710 AC: 29423 AN: 41442

American (AMR) AF: 0.944 AC: 14393 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3262 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3805 AN: 5160

South Asian (SAS) AF: 0.907 AC: 4381 AN: 4830

European-Finnish (FIN) AF: 0.936 AC: 9926 AN: 10602

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64095 AN: 67966

Other (OTH) AF: 0.900 AC: 1903 AN: 2114

Alfa AF: 0.921 Hom.: 27390

Bravo AF: 0.863

Asia WGS AF: 0.837 AC: 2893 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9293474; hg19: chr5-85968134;