rs1359790

Variant names:

• chr13-80143021-G-A
• rs1359790
• ENST00000776551.1:n.142-15689G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-80143021-G-A
• chr13-80143021-G-C
• chr13-80143021-G-T

Variant summary

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

The ENST00000776551.1(LINC01080):​n.142-15689G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,066 control chromosomes in the GnomAD database, including 4,398 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 0.23 (4398 hom., cov: 32)
• Consequence: LINC01080 ENST00000776551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 140 publications found

Genes affected

LINC01080 (HGNC:49123): (long intergenic non-protein coding RNA 1080)

LOC105370275 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776551.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01080	ENST00000776551.1		n.142-15689G>A		intron	N/A
	LINC01080	ENST00000776552.1		n.356-15689G>A		intron	N/A
	LINC01080	ENST00000776553.1		n.56+11509G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34607 AN: 151948 Hom.: 4393 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.228 AC: 34625 AN: 152066 Hom.: 4398 Cov.: 32 AF XY: 0.229 AC XY: 16986 AN XY: 74310

African (AFR) AF: 0.107 AC: 4450 AN: 41520

American (AMR) AF: 0.284 AC: 4335 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1357 AN: 5170

South Asian (SAS) AF: 0.177 AC: 856 AN: 4824

European-Finnish (FIN) AF: 0.282 AC: 2974 AN: 10548

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19029 AN: 67964

Other (OTH) AF: 0.237 AC: 500 AN: 2106

Alfa AF: 0.263 Hom.: 17139

Bravo AF: 0.231

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		0.057

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1359790;

hg19: chr13-80717156;