Genetic Variant ENST00000558874.1:n.190G>A (chr15-94083226-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.100

Publications

6 publications found

Variant links:

Genes affected

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

LINC01581 links:

LOC105369203 (HGNC:):

LOC105369203 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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 link	n.190G>A		non_coding_transcript_exon_variant	Exon 2 of 9
LOC105369203	XR_002957694.2 link	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 link	n.190G>A		non_coding_transcript_exon_variant	Exon 2 of 9	1
LINC01581	ENST00000556357.1 link	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.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.125

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.214

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.306

AC:

46613

AN:

152084

Hom.:

7234

Cov.:

AF XY:

0.308

AC XY:

22887

AN XY:

74330

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.300

AC:

20425

AN:

67988

Other (OTH)

AF:

0.291

AC:

614

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1669

3338

5006

6675

8344

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.80

PhyloP100

0.10

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over