rs584087

Variant names:

• chr18-50866180-C-T
• rs584087
• ENST00000836487.1:n.71+3551C>T

Variant summary

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

The ENST00000836487.1(ENSG00000308800):​n.71+3551C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,068 control chromosomes in the GnomAD database, including 8,224 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as no classification for the single variant (no stars).

• Frequency: Genomes: 𝑓 0.32 (8224 hom., cov: 33)
• Consequence: ENSG00000308800 ENST00000836487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 8 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836487.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308800	ENST00000836487.1		n.71+3551C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48999 AN: 151948 Hom.: 8218 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.322 AC: 49028 AN: 152068 Hom.: 8224 Cov.: 33 AF XY: 0.320 AC XY: 23811 AN XY: 74306

African (AFR) AF: 0.248 AC: 10275 AN: 41478

American (AMR) AF: 0.247 AC: 3769 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1728 AN: 5156

South Asian (SAS) AF: 0.199 AC: 959 AN: 4824

European-Finnish (FIN) AF: 0.432 AC: 4566 AN: 10566

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

European-Non Finnish (NFE) AF: 0.372 AC: 25314 AN: 67988

Other (OTH) AF: 0.308 AC: 650 AN: 2112

Alfa AF: 0.336 Hom.: 3892

Bravo AF: 0.311

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.032
DANN	Benign	0.39
PhyloP100		-2.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs584087;

hg19: chr18-48392550;