rs8001641

Variant names:

• chr13-80118676-G-A
• rs8001641
• ENST00000647704.1:n.2542C>T

Variant summary

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

The ENST00000647704.1(ENSG00000285684):​n.2542C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,996 control chromosomes in the GnomAD database, including 11,862 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 0.36 (11862 hom., cov: 32)
• Consequence: ENSG00000285684 ENST00000647704.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 31 publications found

Genes affected

ENSG00000285684 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647704.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285684	ENST00000647704.1		n.2542C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC01080	ENST00000776551.1		n.142-40034G>A		intron	N/A
	LINC01080	ENST00000776552.1		n.356-40034G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55291 AN: 151878 Hom.: 11864 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.364 AC: 55303 AN: 151996 Hom.: 11862 Cov.: 32 AF XY: 0.360 AC XY: 26730 AN XY: 74272

African (AFR) AF: 0.163 AC: 6776 AN: 41480

American (AMR) AF: 0.340 AC: 5183 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3468

East Asian (EAS) AF: 0.138 AC: 712 AN: 5176

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4826

European-Finnish (FIN) AF: 0.485 AC: 5111 AN: 10530

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.499 AC: 33876 AN: 67944

Other (OTH) AF: 0.368 AC: 778 AN: 2112

Alfa AF: 0.442 Hom.: 43342

Bravo AF: 0.349

Asia WGS AF: 0.190 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	14
DANN	Benign	0.68
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs8001641; hg19: chr13-80692811;