rs9901160

Variant names:

• chr17-18371829-G-A
• rs9901160

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 0.187 in 152,044 control chromosomes in the GnomAD database, including 2,972 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 0.19 (2972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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 (EAS) allele frequency at 95% confidence interval = 0.286 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: 0.187 AC: 28349 AN: 151926 Hom.: 2968 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.187 AC: 28383 AN: 152044 Hom.: 2972 Cov.: 32 AF XY: 0.189 AC XY: 14055 AN XY: 74316

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.167

Alfa AF: 0.143 Hom.: 1852

Bravo AF: 0.194

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9901160; hg19: chr17-18275143;