15-94083226-C-T

Variant names:

• chr15-94083226-C-T
• rs8041151
• ENST00000558874.1:n.190G>A

Variant summary

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

The ENST00000558874.1(LINC01581):​n.190G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,100 control chromosomes in the GnomAD database, including 7,234 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 0.31 (7234 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC01581 ENST00000558874.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 6 publications found

Genes affected

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

LOC105369203 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01581	NR_120320.1	n.190G>A		non_coding_transcript_exon_variant	Exon 2 of 9
LOC105369203	XR_002957694.2	n.181-12579G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01581	ENST00000558874.1	n.190G>A		non_coding_transcript_exon_variant	Exon 2 of 9	1
LINC01581	ENST00000556357.1	n.224G>A		non_coding_transcript_exon_variant	Exon 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46578 AN: 151964 Hom.: 7219 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.295

GnomAD4 exome AF: 0.250 AC: 4 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.306 AC: 46613 AN: 152084 Hom.: 7234 Cov.: 32 AF XY: 0.308 AC XY: 22887 AN XY: 74330

African (AFR) AF: 0.316 AC: 13090 AN: 41476

American (AMR) AF: 0.319 AC: 4872 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3464

East Asian (EAS) AF: 0.445 AC: 2300 AN: 5168

South Asian (SAS) AF: 0.220 AC: 1064 AN: 4826

European-Finnish (FIN) AF: 0.286 AC: 3028 AN: 10574

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20425 AN: 67988

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.303 Hom.: 10704

Bravo AF: 0.312

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.80
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs8041151; hg19: chr15-94626455;