rs11869775

Variant names:

• chr17-13330887-A-G
• rs11869775

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.105 AC: 4362 AN: 41462

American (AMR) AF: 0.144 AC: 2202 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3466

East Asian (EAS) AF: 0.116 AC: 598 AN: 5156

South Asian (SAS) AF: 0.151 AC: 729 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2390 AN: 10514

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16173 AN: 67938

Other (OTH) AF: 0.158 AC: 334 AN: 2114

Alfa AF: 0.219 Hom.: 16409

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

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