rs8039548

Variant names:

• chr15-47808758-G-A
• rs8039548
• ENST00000558792.6:n.415-3880C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558792.6(LINC01491):​n.415-3880C>T variant causes a intron 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 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01491	NR_120336.1	n.283-3880C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.415-3880C>T		intron_variant	Intron 4 of 6	3
LINC01491	ENST00000651940.1	n.279-3880C>T		intron_variant	Intron 3 of 6
LINC01491	ENST00000653152.1	n.319-3880C>T		intron_variant	Intron 3 of 6

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

African (AFR) AF: 0.191 AC: 7900 AN: 41332

American (AMR) AF: 0.134 AC: 2049 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3472

East Asian (EAS) AF: 0.114 AC: 587 AN: 5150

South Asian (SAS) AF: 0.135 AC: 650 AN: 4804

European-Finnish (FIN) AF: 0.0829 AC: 871 AN: 10504

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.128 AC: 8665 AN: 67930

Other (OTH) AF: 0.167 AC: 350 AN: 2096

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
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs8039548; hg19: chr15-48100955;