rs180092

Variant names:

• chr17-69948273-G-A
• rs180092

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 0.251 in 149,388 control chromosomes in the GnomAD database, including 5,164 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 0.25 (5164 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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: 0.251 AC: 37432 AN: 149328 Hom.: 5169 Cov.: 27

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.251 AC: 37437 AN: 149388 Hom.: 5164 Cov.: 27 AF XY: 0.255 AC XY: 18529 AN XY: 72664

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.287

Alfa AF: 0.251 Hom.: 1010

Bravo AF: 0.252

Asia WGS AF: 0.371 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180092; hg19: chr17-67944414;