rs13066666

Variant names:

• chr3-27798376-G-A
• rs13066666
• ENST00000647336.1:n.349+465G>A

Variant summary

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

The ENST00000647336.1(LINC01980):​n.349+465G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 152,180 control chromosomes in the GnomAD database, including 259 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 0.056 (259 hom., cov: 32)
• Consequence: LINC01980 ENST00000647336.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01980	NR_146630.1	n.324+465G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01980	ENST00000647336.1	n.349+465G>A		intron_variant	Intron 1 of 7
LINC01980	ENST00000652951.2	n.350+465G>A		intron_variant	Intron 1 of 5
LINC01980	ENST00000653125.1	n.360+465G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8441 AN: 152062 Hom.: 257 Cov.: 32

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0358

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0636

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0630

Gnomad OTH AF: 0.0551

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

GnomAD4 genome AF: 0.0556 AC: 8456 AN: 152180 Hom.: 259 Cov.: 32 AF XY: 0.0546 AC XY: 4061 AN XY: 74406

African (AFR) AF: 0.0620 AC: 2576 AN: 41530

American (AMR) AF: 0.0358 AC: 547 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0308 AC: 107 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5172

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4826

European-Finnish (FIN) AF: 0.0636 AC: 673 AN: 10584

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0630 AC: 4284 AN: 67996

Other (OTH) AF: 0.0545 AC: 115 AN: 2110

Alfa AF: 0.0574 Hom.: 346

Bravo AF: 0.0547

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.82
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs13066666; hg19: chr3-27839867;