rs9461799

Variant names:

• chr6-32721752-T-C
• rs9461799

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 0.377 in 152,028 control chromosomes in the GnomAD database, including 12,016 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 0.38 (12016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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: 0.377 AC: 57256 AN: 151910 Hom.: 12007 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.377 AC: 57298 AN: 152028 Hom.: 12016 Cov.: 32 AF XY: 0.385 AC XY: 28612 AN XY: 74308

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.377

Alfa AF: 0.425 Hom.: 22199

Bravo AF: 0.364

Asia WGS AF: 0.546 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9461799; hg19: chr6-32689529;