rs1479833

Variant names:

• chr15-94107414-G-A
• rs1479833
• ENST00000558874.1:n.60+465C>T

Variant summary

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

The ENST00000558874.1(LINC01581):​n.60+465C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,094 control chromosomes in the GnomAD database, including 1,957 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 (1957 hom., cov: 33)
• Consequence: LINC01581 ENST00000558874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 1 publications found

Genes affected

LINC01581 (HGNC:51415): (long intergenic non-protein coding RNA 1581)

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 (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558874.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01581	NR_120320.1		n.60+465C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01581	ENST00000558874.1	TSL:1	n.60+465C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22016 AN: 151976 Hom.: 1959 Cov.: 33

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0735

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.145 AC: 22004 AN: 152094 Hom.: 1957 Cov.: 33 AF XY: 0.145 AC XY: 10759 AN XY: 74340

African (AFR) AF: 0.0672 AC: 2788 AN: 41518

American (AMR) AF: 0.217 AC: 3312 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1954 AN: 5144

South Asian (SAS) AF: 0.200 AC: 966 AN: 4820

European-Finnish (FIN) AF: 0.0735 AC: 776 AN: 10562

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10680 AN: 67996

Other (OTH) AF: 0.168 AC: 354 AN: 2110

Alfa AF: 0.163 Hom.: 9488

Bravo AF: 0.155

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.83
PhyloP100		-0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1479833;

hg19: chr15-94650643;