3-184498342-T-C

Variant names:

• chr3-184498342-T-C
• rs3930234
• XR_924788.3:n.326-5418T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_924788.3(LINC01839):​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: LINC01839 XR_924788.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01839	XR_924788.3	n.326-5418T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.848

Alfa AF: 0.843 Hom.: 80270

Bravo AF: 0.856

Asia WGS AF: 0.943 AC: 3277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3930234; hg19: chr3-184216130;