dbSNP rs6802792: LINC00877:n.149-38108A>G (chr3-72138118-T-C) – 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.149-38108A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,170 control chromosomes in the GnomAD database, including 4,467 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 0.14 ( 4467 hom., cov: 32)

Consequence

LINC00877
ENST00000469218.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0350

Publications

0 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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.149-38108A>G	intron_variant	Intron 2 of 8	5
LINC00877	ENST00000481148.5 link	n.132-38108A>G	intron_variant	Intron 1 of 2	4
LINC00877	ENST00000626474.3 link	n.456-38108A>G	intron_variant	Intron 3 of 8	5

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21627

AN:

152052

Hom.:

4438

Cov.:

show subpopulations

Gnomad AFR

AF:

0.455

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0860

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.0615

Gnomad SAS

AF:

0.0498

Gnomad FIN

AF:

0.0431

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00323

Gnomad OTH

AF:

0.115

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

GnomAD4 genome

AF:

0.143

AC:

21725

AN:

152170

Hom.:

4467

Cov.:

AF XY:

0.141

AC XY:

10513

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.456

AC:

18903

AN:

41458

American (AMR)

AF:

0.0862

AC:

1319

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3472

East Asian (EAS)

AF:

0.0610

AC:

316

AN:

5178

South Asian (SAS)

AF:

0.0509

AC:

245

AN:

4816

European-Finnish (FIN)

AF:

0.0431

AC:

457

AN:

10612

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00323

AC:

220

AN:

68022

Other (OTH)

AF:

0.120

AC:

253

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

650

1300

1951

2601

3251

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.0516

Hom.:

1603

Bravo

AF:

0.162

Asia WGS

AF:

0.100

AC:

348

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

1.5

(source)

DANN

Benign

0.58

PhyloP100

0.035

Mutation Taster

=100/0

polymorphism (auto)

(source)

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