3-184498408-C-T

Variant names:

• chr3-184498408-C-T
• rs3930233
• ENST00000827608.1:n.326-5352C>T

Variant summary

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

The ENST00000827608.1(ENSG00000307641):​n.326-5352C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,118 control chromosomes in the GnomAD database, including 36,688 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 0.69 (36688 hom., cov: 33)
• Consequence: ENSG00000307641 ENST00000827608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 4 publications found

Genes affected

ENSG00000307641 (HGNC:):

LINC01839 (HGNC:41330): (long intergenic non-protein coding RNA 1839)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827608.1. 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
	ENSG00000307641	ENST00000827608.1		n.326-5352C>T		intron	N/A
	ENSG00000307641	ENST00000827609.1		n.184-5352C>T		intron	N/A
	ENSG00000307641	ENST00000827610.1		n.166-5352C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104664 AN: 152000 Hom.: 36642 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.689 AC: 104778 AN: 152118 Hom.: 36688 Cov.: 33 AF XY: 0.695 AC XY: 51638 AN XY: 74352

African (AFR) AF: 0.763 AC: 31635 AN: 41462

American (AMR) AF: 0.746 AC: 11413 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2061 AN: 3470

East Asian (EAS) AF: 0.960 AC: 4978 AN: 5188

South Asian (SAS) AF: 0.685 AC: 3299 AN: 4818

European-Finnish (FIN) AF: 0.691 AC: 7310 AN: 10574

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.617 AC: 41964 AN: 67990

Other (OTH) AF: 0.653 AC: 1381 AN: 2116

Alfa AF: 0.639 Hom.: 56153

Bravo AF: 0.699

Asia WGS AF: 0.819 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.070
DANN	Benign	0.59
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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: rs3930233;

hg19: chr3-184216196;