rs17159904

Variant names:

• chr11-86075245-A-G
• rs17159904

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 0.242 in 152,016 control chromosomes in the GnomAD database, including 4,912 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 0.24 (4912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.82
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 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: 0.242 AC: 36699 AN: 151898 Hom.: 4903 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.242 AC: 36732 AN: 152016 Hom.: 4912 Cov.: 32 AF XY: 0.240 AC XY: 17847 AN XY: 74316

African (AFR) AF: 0.282 AC: 11706 AN: 41440

American (AMR) AF: 0.182 AC: 2780 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 935 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5180

South Asian (SAS) AF: 0.0810 AC: 391 AN: 4828

European-Finnish (FIN) AF: 0.344 AC: 3622 AN: 10542

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16551 AN: 67986

Other (OTH) AF: 0.246 AC: 518 AN: 2106

Alfa AF: 0.233 Hom.: 2148

Bravo AF: 0.235

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.1
DANN	Benign	0.83
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs17159904; hg19: chr11-85786287;