ENST00000510907.5:n.282-76393T>G

Variant names:

• chr4-13753387-T-G
• rs2270279
• ENST00000510907.5:n.282-76393T>G

Variant summary

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

The ENST00000510907.5(LINC01182):​n.282-76393T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,102 control chromosomes in the GnomAD database, including 3,103 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 0.20 (3103 hom., cov: 32)
• Consequence: LINC01182 ENST00000510907.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510907.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01182	NR_121681.1		n.282-76393T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01182	ENST00000510907.5	TSL:2	n.282-76393T>G		intron	N/A
	LINC01182	ENST00000669061.1		n.549-76393T>G		intron	N/A
	LINC01182	ENST00000715489.1		n.282-76393T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29964 AN: 151984 Hom.: 3104 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.197 AC: 29984 AN: 152102 Hom.: 3103 Cov.: 32 AF XY: 0.198 AC XY: 14746 AN XY: 74338

African (AFR) AF: 0.235 AC: 9755 AN: 41488

American (AMR) AF: 0.193 AC: 2948 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1030 AN: 5166

South Asian (SAS) AF: 0.105 AC: 508 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2349 AN: 10574

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11905 AN: 67990

Other (OTH) AF: 0.229 AC: 481 AN: 2104

Alfa AF: 0.182 Hom.: 11396

Bravo AF: 0.200

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.099
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2270279; hg19: chr4-13755011;