15-47818455-A-T

Variant names:

• chr15-47818455-A-T
• rs1669832
• ENST00000558792.6:n.309-4279T>A

Variant summary

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

The ENST00000558792.6(LINC01491):​n.309-4279T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,000 control chromosomes in the GnomAD database, including 10,776 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 0.34 (10776 hom., cov: 32)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 0 publications found

Genes affected

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

ENSG00000259754 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01491	NR_120336.1	n.282+9116T>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.309-4279T>A		intron_variant	Intron 3 of 6	3
LINC01491	ENST00000561238.3	n.331-4279T>A		intron_variant	Intron 3 of 3	3
LINC01491	ENST00000651940.1	n.173-4279T>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52001 AN: 151882 Hom.: 10774 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.342 AC: 52015 AN: 152000 Hom.: 10776 Cov.: 32 AF XY: 0.342 AC XY: 25412 AN XY: 74302

African (AFR) AF: 0.100 AC: 4160 AN: 41532

American (AMR) AF: 0.359 AC: 5476 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1468 AN: 3464

East Asian (EAS) AF: 0.348 AC: 1789 AN: 5136

South Asian (SAS) AF: 0.358 AC: 1724 AN: 4812

European-Finnish (FIN) AF: 0.476 AC: 5021 AN: 10554

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31202 AN: 67918

Other (OTH) AF: 0.353 AC: 745 AN: 2112

Alfa AF: 0.396 Hom.: 1639

Bravo AF: 0.323

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1669832; hg19: chr15-48110652;