15-94044188-C-T

Position:

• chr15-94044188-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558874.1(LINC01581):​n.1141+38087G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,022 control chromosomes in the GnomAD database, including 22,333 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 0.53 (22333 hom., cov: 32)
• Consequence: LINC01581 ENST00000558874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

Genes affected

LINC01581 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01581	NR_120320.1	n.1141+38087G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01581	ENST00000558874.1	n.1141+38087G>A		intron_variant		1
LINC01579	ENST00000556447.5	n.409-13787G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79828 AN: 151902 Hom.: 22342 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.525 AC: 79832 AN: 152022 Hom.: 22333 Cov.: 32 AF XY: 0.524 AC XY: 38971 AN XY: 74308

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.517

Alfa AF: 0.575 Hom.: 3222

Bravo AF: 0.514

Asia WGS AF: 0.507 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1351306; hg19: chr15-94587417;