3-184498342-T-C

Variant names:

• chr3-184498342-T-C
• rs3930234
• ENST00000827608.1:n.326-5418T>C

Variant summary

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

The ENST00000827608.1(ENSG00000307641):​n.326-5418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,132 control chromosomes in the GnomAD database, including 55,773 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 0.85 (55773 hom., cov: 31)
• Consequence: ENSG00000307641 ENST00000827608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 13 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 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.326-5418T>C		intron	N/A
	ENSG00000307641	ENST00000827609.1		n.184-5418T>C		intron	N/A
	ENSG00000307641	ENST00000827610.1		n.166-5418T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129963 AN: 152014 Hom.: 55736 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.855 AC: 130058 AN: 152132 Hom.: 55773 Cov.: 31 AF XY: 0.860 AC XY: 63934 AN XY: 74376

African (AFR) AF: 0.850 AC: 35273 AN: 41482

American (AMR) AF: 0.896 AC: 13714 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2804 AN: 3470

East Asian (EAS) AF: 0.978 AC: 5048 AN: 5164

South Asian (SAS) AF: 0.883 AC: 4251 AN: 4814

European-Finnish (FIN) AF: 0.876 AC: 9273 AN: 10588

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56985 AN: 68004

Other (OTH) AF: 0.848 AC: 1789 AN: 2110

Alfa AF: 0.846 Hom.: 125630

Bravo AF: 0.856

Asia WGS AF: 0.943 AC: 3277 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	3.0
DANN	Benign	0.56
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3930234; hg19: chr3-184216130;