rs1993150

Positions:

• chr15-47775321-A-T

Variant summary

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

The ENST00000653152.1(LINC01491):​n.620-913T>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 0.353 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 ENST00000653152.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000653152.1	n.620-913T>A		intron_variant, non_coding_transcript_variant

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;