rs928413

Variant names:

• chr9-6213387-G-A
• rs928413

Your query was ambiguous. Multiple possible variants found:

• chr9-6213387-G-A
• chr9-6213387-G-C
• chr9-6213387-G-T

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 0.682 in 151,794 control chromosomes in the GnomAD database, including 36,468 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 0.68 (36468 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 56 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103459 AN: 151676 Hom.: 36453 Cov.: 29

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.682 AC: 103516 AN: 151794 Hom.: 36468 Cov.: 29 AF XY: 0.684 AC XY: 50721 AN XY: 74192

African (AFR) AF: 0.497 AC: 20525 AN: 41312

American (AMR) AF: 0.761 AC: 11622 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2323 AN: 3468

East Asian (EAS) AF: 0.934 AC: 4819 AN: 5162

South Asian (SAS) AF: 0.761 AC: 3656 AN: 4806

European-Finnish (FIN) AF: 0.740 AC: 7781 AN: 10510

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50561 AN: 67956

Other (OTH) AF: 0.694 AC: 1463 AN: 2108

Alfa AF: 0.721 Hom.: 78721

Bravo AF: 0.672

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.48
DANN	Benign	0.45
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs928413; hg19: chr9-6213387;