rs2581182

Positions:

• chr3-27883105-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647336.1(LINC01980):​n.536-7990C>A variant causes a intron, non coding transcript 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 ENST00000647336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01980	ENST00000647336.1	n.536-7990C>A		intron_variant, non_coding_transcript_variant
LINC01980	ENST00000414382.5	n.337-7990C>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.0951

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0619

Gnomad4 FIN AF: 0.0837

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.128

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2581182; hg19: chr3-27924596;