rs8039548

Positions:

• chr15-47808758-G-A

Variant summary

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

The NR_120336.1(LINC01491):​n.283-3880C>T 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 0.144 in 151,728 control chromosomes in the GnomAD database, including 1,693 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 0.14 (1693 hom., cov: 32)
• Consequence: LINC01491 NR_120336.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669

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 (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01491	NR_120336.1	n.283-3880C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01491	ENST00000653152.1	n.319-3880C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21915 AN: 151610 Hom.: 1691 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0628

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.144 AC: 21924 AN: 151728 Hom.: 1693 Cov.: 32 AF XY: 0.144 AC XY: 10643 AN XY: 74144

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0829

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.167

Alfa AF: 0.146 Hom.: 214

Bravo AF: 0.148

Asia WGS AF: 0.129 AC: 446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8039548; hg19: chr15-48100955;