rs8090593

Variant names:

• chr18-73849723-T-G
• rs8090593
• ENST00000785212.1:n.439+12058T>G

Variant summary

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

The ENST00000785212.1(ENSG00000302257):​n.439+12058T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,132 control chromosomes in the GnomAD database, including 8,785 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 0.31 (8785 hom., cov: 33)
• Consequence: ENSG00000302257 ENST00000785212.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 0 publications found

Genes affected

ENSG00000302257 (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 = 0.517 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
ENSG00000302257	ENST00000785212.1	n.439+12058T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47774 AN: 152014 Hom.: 8786 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.314 AC: 47773 AN: 152132 Hom.: 8785 Cov.: 33 AF XY: 0.323 AC XY: 23997 AN XY: 74350

African (AFR) AF: 0.122 AC: 5053 AN: 41540

American (AMR) AF: 0.384 AC: 5876 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1100 AN: 3462

East Asian (EAS) AF: 0.534 AC: 2752 AN: 5154

South Asian (SAS) AF: 0.455 AC: 2191 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4389 AN: 10564

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

European-Non Finnish (NFE) AF: 0.374 AC: 25460 AN: 67986

Other (OTH) AF: 0.323 AC: 682 AN: 2114

Alfa AF: 0.351 Hom.: 16634

Bravo AF: 0.301

Asia WGS AF: 0.441 AC: 1534 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	0.71
DANN	Benign	0.50
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs8090593; hg19: chr18-71516958;