rs11759809

chr6-50987368-C-T

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/exons	MANE	UniProt

Ensembl

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