13-80133294-A-G

Variant names:

• chr13-80133294-A-G
• rs1215468
• ENST00000776555.1:n.633A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000776555.1(LINC01080):​n.633A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.301 in 152,148 control chromosomes in the GnomAD database, including 6,957 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 0.30 (6957 hom., cov: 33)
• Consequence: LINC01080 ENST00000776555.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.86
• Publications: 23 publications found

Genes affected

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

ENSG00000285684 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370275	XR_942116.3	n.189-11418T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01080	ENST00000776555.1	n.633A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000285684	ENST00000647704.1	n.390+685T>C		intron_variant	Intron 1 of 2
LINC01080	ENST00000776551.1	n.142-25416A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45706 AN: 152030 Hom.: 6944 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.301 AC: 45754 AN: 152148 Hom.: 6957 Cov.: 33 AF XY: 0.299 AC XY: 22257 AN XY: 74374

African (AFR) AF: 0.347 AC: 14403 AN: 41510

American (AMR) AF: 0.316 AC: 4836 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1385 AN: 5160

South Asian (SAS) AF: 0.187 AC: 899 AN: 4814

European-Finnish (FIN) AF: 0.285 AC: 3018 AN: 10586

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19397 AN: 68002

Other (OTH) AF: 0.292 AC: 617 AN: 2114

Alfa AF: 0.290 Hom.: 25627

Bravo AF: 0.314

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	18
DANN	Benign	0.82
PhyloP100		4.9

Splicing

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

Other links and lift over

dbSNP: rs1215468; hg19: chr13-80707429;