rs11759809

Variant names:

• chr6-50987368-C-T
• rs11759809

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 0.285 in 152,012 control chromosomes in the GnomAD database, including 6,629 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 0.29 (6629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.339 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: 0.286 AC: 43368 AN: 151894 Hom.: 6632 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.285 AC: 43379 AN: 152012 Hom.: 6629 Cov.: 32 AF XY: 0.283 AC XY: 20988 AN XY: 74286

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.264

Alfa AF: 0.325 Hom.: 9282

Bravo AF: 0.286

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	1.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11759809; hg19: chr6-50955081;