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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776555.1. 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	ENST00000776555.1		n.633A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000285684	ENST00000647704.1		n.390+685T>C		intron	N/A
	LINC01080	ENST00000776551.1		n.142-25416A>G		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs1215468;

hg19: chr13-80707429;