rs817858

Variant names:

• chr9-107363530-C-G
• rs817858
• XR_001746874.1:n.-185C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-107363530-C-G
• chr9-107363530-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746874.1(LOC107987111):​n.-185C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0404 in 150,068 control chromosomes in the GnomAD database, including 265 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 0.040 (265 hom., cov: 31)
• Consequence: LOC107987111 XR_001746874.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

Genes affected

LOC107987111 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987111	XR_001746874.1	n.-185C>G		upstream_gene_variant
LOC107987111	XR_001746876.1	n.-185C>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0404 AC: 6055 AN: 149956 Hom.: 262 Cov.: 31

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0779

Gnomad FIN AF: 0.0375

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0404 AC: 6062 AN: 150068 Hom.: 265 Cov.: 31 AF XY: 0.0434 AC XY: 3180 AN XY: 73242

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0775

Gnomad4 FIN AF: 0.0375

Gnomad4 NFE AF: 0.0324

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.00335 Hom.: 6

Bravo AF: 0.0454

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.83
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs817858; hg19: chr9-110125811; COSMIC: COSV60388558;