rs867469

Variant names:

• chr9-32383710-G-A
• rs867469

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 0.512 in 152,026 control chromosomes in the GnomAD database, including 20,543 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 0.51 (20543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 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: 0.512 AC: 77736 AN: 151908 Hom.: 20514 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.512 AC: 77819 AN: 152026 Hom.: 20543 Cov.: 32 AF XY: 0.508 AC XY: 37758 AN XY: 74288

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.494

Alfa AF: 0.554 Hom.: 48224

Bravo AF: 0.509

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867469; hg19: chr9-32383708;