chr9-6213387-G-A

Position:

• chr9-6213387-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 0.682 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;