13-80094739-T-C

Variant names:

• chr13-80094739-T-C
• rs9574565
• ENST00000776551.1:n.142-63971T>C

Variant summary

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

The ENST00000776551.1(LINC01080):​n.142-63971T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,994 control chromosomes in the GnomAD database, including 34,133 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 0.65 (34133 hom., cov: 31)
• Consequence: LINC01080 ENST00000776551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 12 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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.142-63971T>C		intron	N/A
	LINC01080	ENST00000776552.1		n.355+19921T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99150 AN: 151876 Hom.: 34131 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.653 AC: 99188 AN: 151994 Hom.: 34133 Cov.: 31 AF XY: 0.650 AC XY: 48316 AN XY: 74286

African (AFR) AF: 0.419 AC: 17369 AN: 41438

American (AMR) AF: 0.758 AC: 11578 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2528 AN: 3466

East Asian (EAS) AF: 0.872 AC: 4495 AN: 5154

South Asian (SAS) AF: 0.666 AC: 3200 AN: 4806

European-Finnish (FIN) AF: 0.659 AC: 6953 AN: 10554

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50709 AN: 67982

Other (OTH) AF: 0.693 AC: 1464 AN: 2114

Alfa AF: 0.715 Hom.: 88777

Bravo AF: 0.656

Asia WGS AF: 0.732 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		-0.13

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: rs9574565;

hg19: chr13-80668874;