rs1561483

Variant names:

• chr15-47777291-A-C
• rs1561483
• ENST00000558792.6:n.572-2883T>G

Variant summary

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

The ENST00000558792.6(LINC01491):​n.572-2883T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,206 control chromosomes in the GnomAD database, including 3,923 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 0.21 (3923 hom., cov: 32)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 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.572-2883T>G		intron_variant	Intron 6 of 6	3
LINC01491	ENST00000651940.1	n.580-2883T>G		intron_variant	Intron 6 of 6
LINC01491	ENST00000653152.1	n.620-2883T>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31822 AN: 152088 Hom.: 3924 Cov.: 32

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.209 AC: 31828 AN: 152206 Hom.: 3923 Cov.: 32 AF XY: 0.214 AC XY: 15947 AN XY: 74402

African (AFR) AF: 0.0741 AC: 3079 AN: 41550

American (AMR) AF: 0.213 AC: 3250 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3470

East Asian (EAS) AF: 0.172 AC: 889 AN: 5176

South Asian (SAS) AF: 0.283 AC: 1366 AN: 4824

European-Finnish (FIN) AF: 0.307 AC: 3255 AN: 10592

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18306 AN: 67994

Other (OTH) AF: 0.224 AC: 473 AN: 2112

Alfa AF: 0.217 Hom.: 572

Bravo AF: 0.196

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.80
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1561483; hg19: chr15-48069488;