Genetic Variant LINC00877:n.149-27364A>T (chr3-72127374-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000469218.6(LINC00877):n.149-27364A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,018 control chromosomes in the GnomAD database, including 7,832 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 0.32 ( 7832 hom., cov: 32)

Consequence

LINC00877
ENST00000469218.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.80

Publications

1 publications found

Variant links:

Genes affected

LINC00877 (HGNC:27706): (long intergenic non-protein coding RNA 877)

LINC00877 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=-0.54).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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
LINC00877	ENST00000469218.6 link	n.149-27364A>T	intron_variant	Intron 2 of 8	5
LINC00877	ENST00000481148.5 link	n.132-27364A>T	intron_variant	Intron 1 of 2	4
LINC00877	ENST00000626474.3 link	n.456-27364A>T	intron_variant	Intron 3 of 8	5

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48309

AN:

151900

Hom.:

7824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.356

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.319

Gnomad EAS

AF:

0.241

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.314

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

GnomAD4 genome

AF:

0.318

AC:

48348

AN:

152018

Hom.:

7832

Cov.:

AF XY:

0.316

AC XY:

23453

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.356

AC:

14743

AN:

41450

American (AMR)

AF:

0.245

AC:

3739

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.319

AC:

1106

AN:

3472

East Asian (EAS)

AF:

0.242

AC:

1248

AN:

5166

South Asian (SAS)

AF:

0.211

AC:

1016

AN:

4820

European-Finnish (FIN)

AF:

0.365

AC:

3855

AN:

10548

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.317

AC:

21578

AN:

67968

Other (OTH)

AF:

0.319

AC:

673

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1687

3374

5060

6747

8434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.317

Hom.:

922

Bravo

AF:

0.312

Asia WGS

AF:

0.237

AC:

825

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

2.8

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