15-47845511-A-G

Variant names:

• chr15-47845511-A-G
• rs671291
• ENST00000558434.2:n.133-546T>C

Variant summary

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

The ENST00000558434.2(LINC01491):​n.133-546T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,086 control chromosomes in the GnomAD database, including 9,207 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 0.29 (9207 hom., cov: 33)
• Consequence: LINC01491 ENST00000558434.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01491	NR_120336.1	n.109-546T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558434.2	n.133-546T>C		intron_variant	Intron 1 of 4	3
LINC01491	ENST00000558792.6	n.123-546T>C		intron_variant	Intron 1 of 6	3
LINC01491	ENST00000561238.3	n.145-546T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43427 AN: 151968 Hom.: 9171 Cov.: 33

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.286 AC: 43522 AN: 152086 Hom.: 9207 Cov.: 33 AF XY: 0.285 AC XY: 21217 AN XY: 74338

African (AFR) AF: 0.581 AC: 24111 AN: 41486

American (AMR) AF: 0.241 AC: 3684 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3468

East Asian (EAS) AF: 0.468 AC: 2414 AN: 5160

South Asian (SAS) AF: 0.271 AC: 1304 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2208 AN: 10574

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8776 AN: 67976

Other (OTH) AF: 0.225 AC: 476 AN: 2112

Alfa AF: 0.166 Hom.: 5361

Bravo AF: 0.301

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.60
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs671291; hg19: chr15-48137708;