rs9467632

Variant names:

• chr6-25889478-A-G
• rs9467632

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 0.0809 in 152,224 control chromosomes in the GnomAD database, including 534 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 0.081 (534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0962 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: 0.0810 AC: 12322 AN: 152106 Hom.: 535 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0479

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0982

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0809 AC: 12315 AN: 152224 Hom.: 534 Cov.: 32 AF XY: 0.0779 AC XY: 5797 AN XY: 74434

Gnomad4 AFR AF: 0.0808

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.0474

Gnomad4 SAS AF: 0.0526

Gnomad4 FIN AF: 0.0478

Gnomad4 NFE AF: 0.0981

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.0901 Hom.: 313

Bravo AF: 0.0839

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.6
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9467632; hg19: chr6-25889706;