rs817858

Variant names:

• chr9-107363530-C-G
• rs817858
• ENST00000761571.1:n.-241C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000761571.1(ENSG00000299203):​n.-241C>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: ENSG00000299203 ENST00000761571.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 10 publications found

Genes affected

ENSG00000299203 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000299203	ENST00000761571.1	n.-241C>G		upstream_gene_variant
ENSG00000299203	ENST00000761572.1	n.-244C>G		upstream_gene_variant
ENSG00000299203	ENST00000761573.1	n.-245C>G		upstream_gene_variant

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

African (AFR) AF: 0.0123 AC: 499 AN: 40424

American (AMR) AF: 0.119 AC: 1791 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.0257 AC: 89 AN: 3464

East Asian (EAS) AF: 0.123 AC: 630 AN: 5108

South Asian (SAS) AF: 0.0775 AC: 367 AN: 4734

European-Finnish (FIN) AF: 0.0375 AC: 383 AN: 10204

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0324 AC: 2197 AN: 67806

Other (OTH) AF: 0.0355 AC: 74 AN: 2082

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

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