rs9285863

Variant names:

• chr5-108735954-T-C
• rs9285863
• ENST00000837376.1:n.-132A>G

Variant summary

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

The ENST00000837376.1(ENSG00000308934):​n.-132A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,176 control chromosomes in the GnomAD database, including 17,159 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 0.43 (17159 hom., cov: 33)
• Consequence: ENSG00000308934 ENST00000837376.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 6 publications found

Genes affected

ENSG00000308934 (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 = 0.731 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
ENSG00000308934	ENST00000837376.1	n.-132A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66072 AN: 152058 Hom.: 17112 Cov.: 33

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.435 AC: 66169 AN: 152176 Hom.: 17159 Cov.: 33 AF XY: 0.426 AC XY: 31674 AN XY: 74416

African (AFR) AF: 0.738 AC: 30633 AN: 41522

American (AMR) AF: 0.282 AC: 4318 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3472

East Asian (EAS) AF: 0.169 AC: 876 AN: 5184

South Asian (SAS) AF: 0.331 AC: 1595 AN: 4826

European-Finnish (FIN) AF: 0.293 AC: 3103 AN: 10590

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22828 AN: 67976

Other (OTH) AF: 0.404 AC: 855 AN: 2114

Alfa AF: 0.380 Hom.: 2493

Bravo AF: 0.446

Asia WGS AF: 0.301 AC: 1047 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	1.6
DANN	Benign	0.61
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9285863; hg19: chr5-108071655;