rs7981942

Variant names:

• chr13-80049211-A-C
• rs7981942
• ENST00000638633.1:n.2181-1978T>G

Your query was ambiguous. Multiple possible variants found:

• chr13-80049211-A-C
• chr13-80049211-A-G
• chr13-80049211-A-T

Variant summary

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

The ENST00000638633.1(ENSG00000284196):​n.2181-1978T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,142 control chromosomes in the GnomAD database, including 7,765 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 (7765 hom., cov: 33)
• Consequence: ENSG00000284196 ENST00000638633.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638
• Publications: 16 publications found

Genes affected

ENSG00000284196 (HGNC:):

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=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638633.1. 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
	ENSG00000284196	ENST00000638633.1	TSL:5	n.2181-1978T>G		intron	N/A
	ENSG00000284196	ENST00000639897.1	TSL:5	n.836-1978T>G		intron	N/A
	ENSG00000284196	ENST00000639965.1	TSL:5	n.523-1978T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44975 AN: 152024 Hom.: 7735 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.296 AC: 45048 AN: 152142 Hom.: 7765 Cov.: 33 AF XY: 0.300 AC XY: 22296 AN XY: 74372

African (AFR) AF: 0.309 AC: 12842 AN: 41514

American (AMR) AF: 0.439 AC: 6699 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3771 AN: 5172

South Asian (SAS) AF: 0.491 AC: 2369 AN: 4824

European-Finnish (FIN) AF: 0.161 AC: 1709 AN: 10598

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15417 AN: 67990

Other (OTH) AF: 0.322 AC: 681 AN: 2112

Alfa AF: 0.261 Hom.: 23722

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	15
DANN	Benign	0.85
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs7981942; hg19: chr13-80623346;