rs4433125

Variant names:

• chr8-143026084-G-A
• rs4433125
• ENST00000809059.1:n.-9C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-143026084-G-A
• chr8-143026084-G-C
• chr8-143026084-G-T

Variant summary

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

The ENST00000809059.1(ENSG00000305146):​n.-9C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,172 control chromosomes in the GnomAD database, including 8,270 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 0.32 (8270 hom., cov: 33)
• Consequence: ENSG00000305146 ENST00000809059.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 4 publications found

Genes affected

ENSG00000305146 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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
ENSG00000305146	ENST00000809059.1	n.-9C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48527 AN: 152054 Hom.: 8256 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.319 AC: 48559 AN: 152172 Hom.: 8270 Cov.: 33 AF XY: 0.320 AC XY: 23818 AN XY: 74410

African (AFR) AF: 0.242 AC: 10054 AN: 41510

American (AMR) AF: 0.378 AC: 5776 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 975 AN: 3470

East Asian (EAS) AF: 0.558 AC: 2886 AN: 5174

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4820

European-Finnish (FIN) AF: 0.400 AC: 4236 AN: 10588

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22497 AN: 68004

Other (OTH) AF: 0.322 AC: 679 AN: 2108

Alfa AF: 0.271 Hom.: 1494

Bravo AF: 0.317

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.49
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4433125; hg19: chr8-144107501;