rs9461799

chr6-32721752-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;