rs1482976

Positions:

• chr3-138942273-G-A

Variant summary

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

The ENST00000495287.1(LINC01391):​n.290+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 ENST00000495287.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

LINC01391 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01391	NR_121649.1	n.290+111C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01391	ENST00000477059.1	n.195+111C>T		intron_variant		3
LINC01391	ENST00000483650.1	n.336+48C>T		intron_variant		3
LINC01391	ENST00000495287.1	n.290+111C>T		intron_variant		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

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.0351

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.0773

Gnomad4 FIN AF: 0.0277

Gnomad4 NFE AF: 0.00788

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0570 Hom.: 1245

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1482976; hg19: chr3-138661115;