rs3118292

Variant names:

• chr9-25143482-A-G
• rs3118292
• ENST00000850879.1:n.213-6187A>G

Variant summary

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

The ENST00000850879.1(ENSG00000309091):​n.213-6187A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 151,668 control chromosomes in the GnomAD database, including 4,720 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 0.23 (4720 hom., cov: 32)
• Consequence: ENSG00000309091 ENST00000850879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 5 publications found

Genes affected

ENSG00000309091 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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
ENSG00000309091	ENST00000850879.1	n.213-6187A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34435 AN: 151552 Hom.: 4703 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.227 AC: 34489 AN: 151668 Hom.: 4720 Cov.: 32 AF XY: 0.223 AC XY: 16507 AN XY: 74134

African (AFR) AF: 0.392 AC: 16236 AN: 41374

American (AMR) AF: 0.144 AC: 2198 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3468

East Asian (EAS) AF: 0.126 AC: 649 AN: 5152

South Asian (SAS) AF: 0.166 AC: 801 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1963 AN: 10560

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11412 AN: 67780

Other (OTH) AF: 0.202 AC: 424 AN: 2100

Alfa AF: 0.184 Hom.: 9568

Bravo AF: 0.232

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.67
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs3118292; hg19: chr9-25143480;