rs8024406

Variant names:

• chr15-47792070-T-C
• rs8024406
• ENST00000558792.6:n.571+11314A>G

Variant summary

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

The ENST00000558792.6(LINC01491):​n.571+11314A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,136 control chromosomes in the GnomAD database, including 4,458 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 0.22 (4458 hom., cov: 33)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 3 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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.571+11314A>G		intron_variant	Intron 6 of 6	3
LINC01491	ENST00000651940.1	n.436-820A>G		intron_variant	Intron 5 of 6
LINC01491	ENST00000653152.1	n.476-820A>G		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32920 AN: 152018 Hom.: 4447 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.217 AC: 32970 AN: 152136 Hom.: 4458 Cov.: 33 AF XY: 0.214 AC XY: 15956 AN XY: 74406

African (AFR) AF: 0.372 AC: 15441 AN: 41466

American (AMR) AF: 0.210 AC: 3203 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 803 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1725 AN: 5168

South Asian (SAS) AF: 0.192 AC: 926 AN: 4822

European-Finnish (FIN) AF: 0.0870 AC: 923 AN: 10608

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9346 AN: 68010

Other (OTH) AF: 0.228 AC: 482 AN: 2114

Alfa AF: 0.165 Hom.: 8861

Bravo AF: 0.230

Asia WGS AF: 0.312 AC: 1082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	10
DANN	Benign	0.88
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs8024406; hg19: chr15-48084267;