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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.682 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

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.694

Alfa AF: 0.717 Hom.: 16490

Bravo AF: 0.672

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928413; hg19: chr9-6213387;