chr4-14163091-T-A

Variant names:

• chr4-14163091-T-A
• rs6449004
• ENST00000715490.1:n.447-79555T>A

Variant summary

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

The ENST00000715490.1(LINC01182):​n.447-79555T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,860 control chromosomes in the GnomAD database, including 35,558 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 0.68 (35558 hom., cov: 31)
• Consequence: LINC01182 ENST00000715490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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	ENST00000715490.1	n.447-79555T>A		intron_variant	Intron 3 of 3
LINC01182	ENST00000715511.1	n.285+7026T>A		intron_variant	Intron 2 of 2
LINC01182	ENST00000727466.1	n.573+69732T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102806 AN: 151742 Hom.: 35501 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.678 AC: 102921 AN: 151860 Hom.: 35558 Cov.: 31 AF XY: 0.682 AC XY: 50657 AN XY: 74230

African (AFR) AF: 0.778 AC: 32248 AN: 41466

American (AMR) AF: 0.710 AC: 10836 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2441 AN: 3462

East Asian (EAS) AF: 0.908 AC: 4683 AN: 5158

South Asian (SAS) AF: 0.657 AC: 3156 AN: 4804

European-Finnish (FIN) AF: 0.642 AC: 6789 AN: 10572

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.600 AC: 40673 AN: 67830

Other (OTH) AF: 0.678 AC: 1427 AN: 2106

Alfa AF: 0.648 Hom.: 4026

Bravo AF: 0.688

Asia WGS AF: 0.790 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs6449004; hg19: chr4-14164715;