rs9466056

Variant names:

• chr6-21384382-A-G
• rs9466056

Your query was ambiguous. Multiple possible variants found:

• chr6-21384382-A-G
• chr6-21384382-A-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 0.612 in 151,992 control chromosomes in the GnomAD database, including 28,513 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 0.61 (28513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.612 AC: 92915 AN: 151874 Hom.: 28482 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.612 AC: 93005 AN: 151992 Hom.: 28513 Cov.: 32 AF XY: 0.610 AC XY: 45296 AN XY: 74310

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.585

Alfa AF: 0.609 Hom.: 41725

Bravo AF: 0.607

Asia WGS AF: 0.654 AC: 2273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9466056; hg19: chr6-21384613;