ENST00000510907.5:n.282-43088A>G

Variant names:

• chr4-13786692-A-G
• rs1019271
• ENST00000510907.5:n.282-43088A>G

Variant summary

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

The ENST00000510907.5(LINC01182):​n.282-43088A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,870 control chromosomes in the GnomAD database, including 24,955 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 0.56 (24955 hom., cov: 31)
• Consequence: LINC01182 ENST00000510907.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 5 publications found

Genes affected

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

ENSG00000288951 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01182	NR_121681.1	n.282-43088A>G		intron_variant	Intron 2 of 3
LOC101929048	XR_001741385.2	n.434+303T>C		intron_variant	Intron 3 of 3
LOC101929048	XR_001741386.2	n.303-999T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01182	ENST00000510907.5	n.282-43088A>G		intron_variant	Intron 2 of 3	2
LINC01182	ENST00000669061.1	n.549-43088A>G		intron_variant	Intron 2 of 4
ENSG00000288951	ENST00000689499.3	n.193-19732T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85056 AN: 151750 Hom.: 24946 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.560 AC: 85082 AN: 151870 Hom.: 24955 Cov.: 31 AF XY: 0.557 AC XY: 41385 AN XY: 74238

African (AFR) AF: 0.370 AC: 15302 AN: 41400

American (AMR) AF: 0.573 AC: 8743 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2352 AN: 3470

East Asian (EAS) AF: 0.494 AC: 2546 AN: 5152

South Asian (SAS) AF: 0.664 AC: 3181 AN: 4794

European-Finnish (FIN) AF: 0.593 AC: 6243 AN: 10536

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44625 AN: 67944

Other (OTH) AF: 0.596 AC: 1258 AN: 2112

Alfa AF: 0.629 Hom.: 51991

Bravo AF: 0.550

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.65
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1019271; hg19: chr4-13788316;