rs4680882

Variant names:

• chr3-27801877-G-A
• rs4680882
• ENST00000647336.1:n.350-887G>A

Variant summary

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

The NR_146630.1(LINC01980):​n.325-887G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,988 control chromosomes in the GnomAD database, including 7,308 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 (7308 hom., cov: 32)
• Consequence: LINC01980 NR_146630.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• 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=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_146630.1. 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
	LINC01980	NR_146630.1		n.325-887G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01980	ENST00000647336.1		n.350-887G>A		intron	N/A
	LINC01980	ENST00000652951.2		n.351-887G>A		intron	N/A
	LINC01980	ENST00000653125.1		n.361-237G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45952 AN: 151870 Hom.: 7290 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.303 AC: 46019 AN: 151988 Hom.: 7308 Cov.: 32 AF XY: 0.307 AC XY: 22802 AN XY: 74264

African (AFR) AF: 0.329 AC: 13627 AN: 41462

American (AMR) AF: 0.342 AC: 5229 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 914 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2844 AN: 5148

South Asian (SAS) AF: 0.288 AC: 1386 AN: 4814

European-Finnish (FIN) AF: 0.333 AC: 3512 AN: 10544

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17540 AN: 67962

Other (OTH) AF: 0.296 AC: 624 AN: 2110

Alfa AF: 0.267 Hom.: 2417

Bravo AF: 0.305

Asia WGS AF: 0.414 AC: 1439 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	0.61
DANN	Benign	0.51
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4680882; hg19: chr3-27843368;