rs6847349

Variant names:

• chr4-14039299-G-A
• rs6847349
• ENST00000715489.1:n.728-22965G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-14039299-G-A
• chr4-14039299-G-C
• chr4-14039299-G-T

Variant summary

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

The ENST00000715489.1(LINC01182):​n.728-22965G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 135,010 control chromosomes in the GnomAD database, including 18,571 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 0.52 (18571 hom., cov: 22)
• Consequence: LINC01182 ENST00000715489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 3 publications found

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

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 = 0.805 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
LINC01182	ENST00000715489.1	n.728-22965G>A		intron_variant	Intron 5 of 8
LINC01182	ENST00000715490.1	n.342+2863G>A		intron_variant	Intron 2 of 3
LINC01182	ENST00000715491.1	n.183-22965G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.523 AC: 70515 AN: 134950 Hom.: 18561 Cov.: 22

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.522 AC: 70539 AN: 135010 Hom.: 18571 Cov.: 22 AF XY: 0.528 AC XY: 34434 AN XY: 65178

African (AFR) AF: 0.326 AC: 10658 AN: 32698

American (AMR) AF: 0.688 AC: 9387 AN: 13652

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1605 AN: 3296

East Asian (EAS) AF: 0.826 AC: 4012 AN: 4856

South Asian (SAS) AF: 0.518 AC: 2213 AN: 4270

European-Finnish (FIN) AF: 0.618 AC: 5330 AN: 8620

Middle Eastern (MID) AF: 0.596 AC: 143 AN: 240

European-Non Finnish (NFE) AF: 0.555 AC: 35865 AN: 64658

Other (OTH) AF: 0.533 AC: 997 AN: 1872

Alfa AF: 0.494 Hom.: 9009

Bravo AF: 0.482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.76
DANN	Benign	0.59
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6847349; hg19: chr4-14040923; COSMIC: COSV69990087;