rs1860189

Variant names:

• chr17-34251339-A-G
• rs1860189

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 0.149 in 152,196 control chromosomes in the GnomAD database, including 1,793 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 0.15 (1793 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 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: 0.150 AC: 22748 AN: 152078 Hom.: 1793 Cov.: 32

Gnomad AFR AF: 0.0906

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.149 AC: 22740 AN: 152196 Hom.: 1793 Cov.: 32 AF XY: 0.150 AC XY: 11149 AN XY: 74400

Gnomad4 AFR AF: 0.0905

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.165

Alfa AF: 0.158 Hom.: 309

Bravo AF: 0.146

Asia WGS AF: 0.167 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1860189; hg19: chr17-32578358;