ENST00000446687.1:n.236-5070A>G

Variant names:

• chr1-167187263-T-C
• rs9803659
• ENST00000446687.1:n.236-5070A>G

Variant summary

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

The ENST00000446687.1(LINC01363):​n.236-5070A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,000 control chromosomes in the GnomAD database, including 9,919 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 0.36 (9919 hom., cov: 32)
• Consequence: LINC01363 ENST00000446687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 15 publications found

Genes affected

LINC01363 (HGNC:50598): (long intergenic non-protein coding RNA 1363)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446687.1. 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
	LINC01363	NR_110811.1		n.249-5070A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01363	ENST00000446687.1	TSL:1	n.236-5070A>G		intron	N/A
	LINC01363	ENST00000426709.5	TSL:5	n.201-5070A>G		intron	N/A
	LINC01363	ENST00000428030.5	TSL:3	n.188+7795A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54288 AN: 151882 Hom.: 9908 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.357 AC: 54332 AN: 152000 Hom.: 9919 Cov.: 32 AF XY: 0.354 AC XY: 26324 AN XY: 74316

African (AFR) AF: 0.368 AC: 15249 AN: 41444

American (AMR) AF: 0.330 AC: 5048 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1459 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1351 AN: 5166

South Asian (SAS) AF: 0.266 AC: 1285 AN: 4824

European-Finnish (FIN) AF: 0.312 AC: 3299 AN: 10558

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25506 AN: 67940

Other (OTH) AF: 0.349 AC: 738 AN: 2116

Alfa AF: 0.368 Hom.: 48594

Bravo AF: 0.360

Asia WGS AF: 0.254 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.54
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9803659; hg19: chr1-167156500;