18-50872497-G-A

Variant names:

• chr18-50872497-G-A
• rs585344
• ENST00000836487.1:n.*227G>A

Variant summary

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

The ENST00000836487.1(ENSG00000308800):​n.*227G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,028 control chromosomes in the GnomAD database, including 8,148 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 (8148 hom., cov: 32)
• Consequence: ENSG00000308800 ENST00000836487.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.677
• Publications: 3 publications found

Genes affected

ENSG00000308800 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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
ENSG00000308800	ENST00000836487.1	n.*227G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48784 AN: 151910 Hom.: 8143 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.321 AC: 48810 AN: 152028 Hom.: 8148 Cov.: 32 AF XY: 0.319 AC XY: 23686 AN XY: 74318

African (AFR) AF: 0.246 AC: 10194 AN: 41448

American (AMR) AF: 0.245 AC: 3738 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1164 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1714 AN: 5162

South Asian (SAS) AF: 0.199 AC: 961 AN: 4832

European-Finnish (FIN) AF: 0.432 AC: 4559 AN: 10562

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25253 AN: 67972

Other (OTH) AF: 0.309 AC: 650 AN: 2106

Alfa AF: 0.340 Hom.: 1196

Bravo AF: 0.309

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.6
DANN	Benign	0.75
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs585344; hg19: chr18-48398867; COSMIC: COSV69621494;