Genetic Variant LINC00881:n.204-1469C>T (chr3-157167548-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 ENST00000480817.1(LINC00881):n.204-1469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,950 control chromosomes in the GnomAD database, including 12,630 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 0.40 ( 12630 hom., cov: 32)

Consequence

LINC00881
ENST00000480817.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.105

Publications

7 publications found

Variant links:

Genes affected

LINC00881 (HGNC:48567): (long intergenic non-protein coding RNA 881)

LINC00881 links:

ENSG00000301840 (HGNC:):

ENSG00000301840 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00881	ENST00000480817.1 link	n.204-1469C>T	intron_variant	Intron 1 of 1	3
LINC00881	ENST00000781925.1 link	n.342-1469C>T	intron_variant	Intron 2 of 4
LINC00881	ENST00000781926.1 link	n.510-1469C>T	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.400

AC:

60683

AN:

151832

Hom.:

12611

Cov.:

show subpopulations

Gnomad AFR

AF:

0.440

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.559

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.577

Gnomad SAS

AF:

0.404

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.390

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

GnomAD4 genome

AF:

0.400

AC:

60749

AN:

151950

Hom.:

12630

Cov.:

AF XY:

0.404

AC XY:

29975

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.440

AC:

18232

AN:

41412

American (AMR)

AF:

0.559

AC:

8543

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.326

AC:

1128

AN:

3464

East Asian (EAS)

AF:

0.577

AC:

2974

AN:

5158

South Asian (SAS)

AF:

0.404

AC:

1945

AN:

4820

European-Finnish (FIN)

AF:

0.299

AC:

3157

AN:

10548

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.344

AC:

23396

AN:

67952

Other (OTH)

AF:

0.390

AC:

825

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1805

3610

5414

7219

9024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

554

1108

1662

2216

2770

<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:

0.369

Hom.:

1720

Bravo

AF:

0.425

Asia WGS

AF:

0.505

AC:

1752

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

9.8

(source)

DANN

Benign

0.75

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