chr15-94038713-A-C

Variant names:

• chr15-94038713-A-C
• rs12101726
• ENST00000558874.1:n.1142-36954T>G

Variant summary

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

The ENST00000558874.1(LINC01581):​n.1142-36954T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,144 control chromosomes in the GnomAD database, including 5,692 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 0.19 (5692 hom., cov: 32)
• Consequence: LINC01581 ENST00000558874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 3 publications found

Genes affected

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

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01581	NR_120320.1	n.1142-36954T>G		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01581	ENST00000558874.1	n.1142-36954T>G		intron_variant	Intron 2 of 8	1
LINC01579	ENST00000556447.5	n.409-8312T>G		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28962 AN: 152026 Hom.: 5659 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.191 AC: 29053 AN: 152144 Hom.: 5692 Cov.: 32 AF XY: 0.188 AC XY: 13958 AN XY: 74408

African (AFR) AF: 0.500 AC: 20720 AN: 41434

American (AMR) AF: 0.139 AC: 2118 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 277 AN: 3472

East Asian (EAS) AF: 0.169 AC: 876 AN: 5182

South Asian (SAS) AF: 0.169 AC: 817 AN: 4822

European-Finnish (FIN) AF: 0.0132 AC: 140 AN: 10620

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0535 AC: 3637 AN: 68012

Other (OTH) AF: 0.180 AC: 380 AN: 2112

Alfa AF: 0.0983 Hom.: 6844

Bravo AF: 0.215

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.30
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12101726; hg19: chr15-94581942;