rs9469220

Variant names:

• chr6-32690533-G-A
• rs9469220

Your query was ambiguous. Multiple possible variants found:

• chr6-32690533-G-A
• chr6-32690533-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 0.531 in 151,794 control chromosomes in the GnomAD database, including 21,624 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 0.53 (21624 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 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: 0.531 AC: 80536 AN: 151676 Hom.: 21609 Cov.: 31

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.531 AC: 80594 AN: 151794 Hom.: 21624 Cov.: 31 AF XY: 0.532 AC XY: 39429 AN XY: 74164

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.578

Alfa AF: 0.515 Hom.: 20786

Bravo AF: 0.536

Asia WGS AF: 0.643 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9469220; hg19: chr6-32658310;