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. The variant received -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
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.624 AC: 25845 AN: 41428

American (AMR) AF: 0.561 AC: 8566 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3132 AN: 5168

South Asian (SAS) AF: 0.560 AC: 2699 AN: 4818

European-Finnish (FIN) AF: 0.630 AC: 6657 AN: 10566

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42196 AN: 67958

Other (OTH) AF: 0.585 AC: 1234 AN: 2110

Alfa AF: 0.609 Hom.: 59683

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs9466056; hg19: chr6-21384613;