rs1993150

Variant names:

• chr15-47775321-A-T
• rs1993150
• ENST00000558792.6:n.572-913T>A

Variant summary

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

The ENST00000558792.6(LINC01491):​n.572-913T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,014 control chromosomes in the GnomAD database, including 10,094 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 0.35 (10094 hom., cov: 32)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

Genes affected

LINC01491 (HGNC:51148): (long intergenic non-protein coding RNA 1491)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.572-913T>A		intron_variant	Intron 6 of 6	3
LINC01491	ENST00000651940.1	n.580-913T>A		intron_variant	Intron 6 of 6
LINC01491	ENST00000653152.1	n.620-913T>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53536 AN: 151896 Hom.: 10085 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.352 AC: 53585 AN: 152014 Hom.: 10094 Cov.: 32 AF XY: 0.362 AC XY: 26923 AN XY: 74282

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.370

Alfa AF: 0.323 Hom.: 994

Bravo AF: 0.357

Asia WGS AF: 0.557 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1993150; hg19: chr15-48067518;