rs1561483

chr15-47777291-A-C

Variant summary

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

The ENST00000653152.1(LINC01491):n.620-2883T>G 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 0.209 in 152,206 control chromosomes in the GnomAD database, including 3,923 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 0.21 (3923 hom., cov: 32)
• Consequence: LINC01491 ENST00000653152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01491	ENST00000653152.1	n.620-2883T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31822 AN: 152088 Hom.: 3924 Cov.: 32

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.209 AC: 31828 AN: 152206 Hom.: 3923 Cov.: 32 AF XY: 0.214 AC XY: 15947 AN XY: 74402

Gnomad4 AFR AF: 0.0741

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.224

Alfa AF: 0.221 Hom.: 569

Bravo AF: 0.196

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1561483; hg19: chr15-48069488;