Genetic Variant LINC02778:n.150-16909G>A (chr1-60225916-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 XR_947430.2(LINC02778):n.150-16909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,712 control chromosomes in the GnomAD database, including 1,854 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 0.15 ( 1854 hom., cov: 31)

Consequence

LINC02778
XR_947430.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.603

Publications

1 publications found

Variant links:

Genes affected

LINC02778 (HGNC:54298): (long intergenic non-protein coding RNA 2778)

LINC02778 links:

LOC105378761 (HGNC:):

LOC105378761 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02778	XR_947430.2 link	n.150-16909G>A		intron_variant	Intron 1 of 4
LOC105378761	XR_947431.2 link	n.617+25671C>T		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22797

AN:

151592

Hom.:

1856

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.201

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.137

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

GnomAD4 genome

AF:

0.150

AC:

22814

AN:

151712

Hom.:

1854

Cov.:

AF XY:

0.153

AC XY:

11317

AN XY:

74124

show subpopulations

African (AFR)

AF:

0.210

AC:

8673

AN:

41344

American (AMR)

AF:

0.196

AC:

2981

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

356

AN:

3468

East Asian (EAS)

AF:

0.188

AC:

956

AN:

5086

South Asian (SAS)

AF:

0.120

AC:

577

AN:

4802

European-Finnish (FIN)

AF:

0.174

AC:

1826

AN:

10508

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6943

AN:

67942

Other (OTH)

AF:

0.136

AC:

287

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

929

1858

2788

3717

4646

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.119

Hom.:

5290

Bravo

AF:

0.160

Asia WGS

AF:

0.174

AC:

605

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.42

(source)

DANN

Benign

0.49

PhyloP100

-0.60

Splicing

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

Publications

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1-60225916-G-A

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