Genetic Variant LINC00881:n.168-10363G>A (chr3-157229227-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000460796.2(LINC00881):n.168-10363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,244 control chromosomes in the GnomAD database, including 660 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 0.055 ( 660 hom., cov: 32)

Consequence

LINC00881
ENST00000460796.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.404

Variant links:

Genes affected

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

LINC00881 links:

LOC101928236 (HGNC:):

LOC101928236 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928236	XR_007096141.1 link	n.1498-10363G>A		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00881	ENST00000460796.2 link	n.168-10363G>A	intron_variant	Intron 1 of 1	3
LINC00881	ENST00000487238.5 link	n.122-10363G>A	intron_variant	Intron 1 of 2	4
LINC00881	ENST00000488040.6 link	n.181-10363G>A	intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.0547

AC:

8315

AN:

152126

Hom.:

662

Cov.:

show subpopulations

Gnomad AFR

AF:

0.177

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0226

Gnomad ASJ

AF:

0.0176

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00891

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00611

Gnomad OTH

AF:

0.0450

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

GnomAD4 genome

AF:

0.0547

AC:

8330

AN:

152244

Hom.:

660

Cov.:

AF XY:

0.0536

AC XY:

3987

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.177

AC:

7342

AN:

41516

American (AMR)

AF:

0.0225

AC:

345

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0176

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.00975

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00132

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00612

AC:

416

AN:

68022

Other (OTH)

AF:

0.0445

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

368

736

1103

1471

1839

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0172

Hom.:

Bravo

AF:

0.0602

Asia WGS

AF:

0.0100

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

9.1

(source)

DANN

Benign

0.67

PhyloP100

0.40

Splicing

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

Publications

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chr3-157229227-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over