rs1482976

Variant names:

• chr3-138942273-G-A
• rs1482976
• ENST00000477059.2:n.284+111C>T

Variant summary

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

The ENST00000477059.2(LINC01391):​n.284+111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,218 control chromosomes in the GnomAD database, including 3,738 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 0.15 (3738 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01391 ENST00000477059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 1 publications found

Genes affected

LINC01391 (HGNC:50666): (long intergenic non-protein coding RNA 1391)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01391	NR_121649.1	n.290+111C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01391	ENST00000477059.2	n.284+111C>T		intron_variant	Intron 2 of 2	3
LINC01391	ENST00000483650.1	n.336+48C>T		intron_variant	Intron 2 of 2	3
LINC01391	ENST00000495287.1	n.290+111C>T		intron_variant	Intron 2 of 2	2
LINC01391	ENST00000774123.1	n.344+48C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22063 AN: 152100 Hom.: 3731 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00788

Gnomad OTH AF: 0.141

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.145 AC: 22126 AN: 152218 Hom.: 3738 Cov.: 33 AF XY: 0.148 AC XY: 11041 AN XY: 74438

African (AFR) AF: 0.336 AC: 13941 AN: 41508

American (AMR) AF: 0.230 AC: 3519 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0351 AC: 122 AN: 3472

East Asian (EAS) AF: 0.582 AC: 3005 AN: 5162

South Asian (SAS) AF: 0.0773 AC: 373 AN: 4826

European-Finnish (FIN) AF: 0.0277 AC: 294 AN: 10612

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

European-Non Finnish (NFE) AF: 0.00788 AC: 536 AN: 68026

Other (OTH) AF: 0.145 AC: 307 AN: 2112

Alfa AF: 0.0706 Hom.: 2004

Bravo AF: 0.176

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1482976; hg19: chr3-138661115;