Genetic Variant LINC02770:n.225+15488G>C (chr1-191748398-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_186758.1(LINC02770):n.225+15488G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 151,884 control chromosomes in the GnomAD database, including 53,525 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 0.84 ( 53525 hom., cov: 32)

Consequence

LINC02770
NR_186758.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.90

Publications

2 publications found

Variant links:

Genes affected

LINC02770 (HGNC:54290): (long intergenic non-protein coding RNA 2770)

LINC02770 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=-1.08).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02770	NR_186758.1 link	n.225+15488G>C		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.838

AC:

127168

AN:

151762

Hom.:

53462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.864

Gnomad AMI

AF:

0.746

Gnomad AMR

AF:

0.857

Gnomad ASJ

AF:

0.800

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.913

Gnomad FIN

AF:

0.821

Gnomad MID

AF:

0.758

Gnomad NFE

AF:

0.807

Gnomad OTH

AF:

0.819

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

GnomAD4 genome

AF:

0.838

AC:

127289

AN:

151884

Hom.:

53525

Cov.:

AF XY:

0.843

AC XY:

62565

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.865

AC:

35685

AN:

41274

American (AMR)

AF:

0.857

AC:

13095

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.800

AC:

2773

AN:

3468

East Asian (EAS)

AF:

0.997

AC:

5151

AN:

5166

South Asian (SAS)

AF:

0.913

AC:

4391

AN:

4808

European-Finnish (FIN)

AF:

0.821

AC:

8686

AN:

10582

Middle Eastern (MID)

AF:

0.748

AC:

220

AN:

294

European-Non Finnish (NFE)

AF:

0.807

AC:

54874

AN:

67998

Other (OTH)

AF:

0.821

AC:

1735

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1055

2109

3164

4218

5273

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.776

Hom.:

2385

Bravo

AF:

0.839

Asia WGS

AF:

0.937

AC:

3258

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.050

(source)

DANN

Benign

0.36

PhyloP100

-2.9

Splicing

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

Publications

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1-191748398-G-C

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