rs11869775

chr17-13330887-A-G

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 0.183 in 151,946 control chromosomes in the GnomAD database, including 2,827 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 0.18 (2827 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.183 AC: 27829 AN: 151828 Hom.: 2826 Cov.: 30

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.183 AC: 27842 AN: 151946 Hom.: 2827 Cov.: 30 AF XY: 0.180 AC XY: 13374 AN XY: 74246

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.158

Alfa AF: 0.222 Hom.: 7948

Bravo AF: 0.174

Asia WGS AF: 0.118 AC: 412 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.14
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11869775; hg19: chr17-13234204; COSMIC: COSV60074215;