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: 139 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370275	XR_942116.3	n.189-21145C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01080	ENST00000776551.1	n.142-15689G>A		intron_variant	Intron 1 of 1
LINC01080	ENST00000776552.1	n.356-15689G>A		intron_variant	Intron 1 of 1
LINC01080	ENST00000776553.1	n.56+11509G>A		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs1359790; hg19: chr13-80717156;