rs11080058

chr17-28415042-G-A

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 0.32 in 152,058 control chromosomes in the GnomAD database, including 8,105 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 0.32 (8105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.320 AC: 48639 AN: 151940 Hom.: 8093 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.320 AC: 48674 AN: 152058 Hom.: 8105 Cov.: 32 AF XY: 0.320 AC XY: 23754 AN XY: 74306

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.329

Alfa AF: 0.290 Hom.: 11992

Bravo AF: 0.333

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.041
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11080058; hg19: chr17-26742060;