rs9467632

Variant names:

• chr6-25889478-A-G
• rs9467632

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 0.0809 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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0808 AC: 3356 AN: 41540

American (AMR) AF: 0.0626 AC: 957 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3466

East Asian (EAS) AF: 0.0474 AC: 246 AN: 5190

South Asian (SAS) AF: 0.0526 AC: 254 AN: 4830

European-Finnish (FIN) AF: 0.0478 AC: 507 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0981 AC: 6671 AN: 67980

Other (OTH) AF: 0.0743 AC: 157 AN: 2114

Alfa AF: 0.0965 Hom.: 647

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
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs9467632; hg19: chr6-25889706;