13-91089667-C-T

Variant names:

• chr13-91089667-C-T
• rs898271
• NR_104057.1:n.22-50G>A

Variant summary

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

The NR_104057.1(LINC00380):​n.22-50G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 151,976 control chromosomes in the GnomAD database, including 29,305 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 0.61 (29305 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00380 NR_104057.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 6 publications found

Genes affected

LINC00380 (HGNC:42706): (long intergenic non-protein coding RNA 380)

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 = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_104057.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00380	NR_104057.1		n.22-50G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00380	ENST00000442478.2	TSL:2	n.-3G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92114 AN: 151858 Hom.: 29244 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.607 AC: 92234 AN: 151976 Hom.: 29305 Cov.: 32 AF XY: 0.617 AC XY: 45864 AN XY: 74280

African (AFR) AF: 0.721 AC: 29895 AN: 41472

American (AMR) AF: 0.624 AC: 9537 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1662 AN: 3464

East Asian (EAS) AF: 0.982 AC: 5084 AN: 5178

South Asian (SAS) AF: 0.787 AC: 3790 AN: 4814

European-Finnish (FIN) AF: 0.613 AC: 6454 AN: 10524

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34103 AN: 67938

Other (OTH) AF: 0.552 AC: 1165 AN: 2110

Alfa AF: 0.539 Hom.: 83192

Bravo AF: 0.609

Asia WGS AF: 0.852 AC: 2963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.4
DANN	Benign	0.65
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs898271; hg19: chr13-91741921;