rs13066666

chr3-27798376-G-A

Variant summary

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

The NR_146630.1(LINC01980):n.324+465G>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 0.0556 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 NR_146630.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

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=-0.97).
• 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/exons	MANE	UniProt
LINC01980	NR_146630.1	n.324+465G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01980	ENST00000647336.1	n.349+465G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0620

Gnomad4 AMR AF: 0.0358

Gnomad4 ASJ AF: 0.0308

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0178

Gnomad4 FIN AF: 0.0636

Gnomad4 NFE AF: 0.0630

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.0571 Hom.: 217

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13066666; hg19: chr3-27839867;