rs2581182

Variant names:

• chr3-27883105-C-A
• rs2581182
• ENST00000414382.5:n.337-7990C>A

Variant summary

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

The ENST00000414382.5(LINC01980):​n.337-7990C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,966 control chromosomes in the GnomAD database, including 1,257 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 0.13 (1257 hom., cov: 31)
• Consequence: LINC01980 ENST00000414382.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 1 publications found

Genes affected

LINC01980 (HGNC:52808): (long intergenic non-protein coding RNA 1980)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414382.5. 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
	LINC01980	ENST00000414382.5	TSL:4	n.337-7990C>A		intron	N/A
	LINC01980	ENST00000647336.1		n.536-7990C>A		intron	N/A
	LINC01980	ENST00000746453.1		n.306-24843C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19112 AN: 151846 Hom.: 1253 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0921

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0620

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.126 AC: 19141 AN: 151966 Hom.: 1257 Cov.: 31 AF XY: 0.122 AC XY: 9061 AN XY: 74270

African (AFR) AF: 0.163 AC: 6734 AN: 41432

American (AMR) AF: 0.0918 AC: 1402 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0951 AC: 330 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1005 AN: 5162

South Asian (SAS) AF: 0.0619 AC: 298 AN: 4818

European-Finnish (FIN) AF: 0.0837 AC: 882 AN: 10538

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8005 AN: 67962

Other (OTH) AF: 0.128 AC: 269 AN: 2108

Alfa AF: 0.123 Hom.: 183

Bravo AF: 0.129

Asia WGS AF: 0.132 AC: 460 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		0.071

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: rs2581182;

hg19: chr3-27924596;