15-94083226-C-T

Position:

• chr15-94083226-C-T

Variant summary

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

The NR_120320.1(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 NR_120320.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

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

LOC105369203 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01581	NR_120320.1	n.190G>A		non_coding_transcript_exon_variant	2/9
LOC105369203	XR_002957694.2	n.181-12579G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01581	ENST00000558874.1	n.190G>A		non_coding_transcript_exon_variant	2/9	1
LINC01581	ENST00000556357.1	n.224G>A		non_coding_transcript_exon_variant	2/2	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

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.214

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

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.291

Alfa AF: 0.300 Hom.: 7315

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8041151; hg19: chr15-94626455;