Genetic Variant LINC01122:n.1150+25330A>G (chr2-59161556-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000422723.6(LINC01122):n.1150+25330A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,036 control chromosomes in the GnomAD database, including 10,056 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 0.36 ( 10056 hom., cov: 32)

Consequence

LINC01122
ENST00000422723.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

3 publications found

Variant links:

Genes affected

LINC01122 (HGNC:49267): (long intergenic non-protein coding RNA 1122)

LINC01122 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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
LINC01122	ENST00000422723.6 link	n.1150+25330A>G	intron_variant	Intron 10 of 10	3
LINC01122	ENST00000650010.2 link	n.2172+25330A>G	intron_variant	Intron 13 of 14
LINC01122	ENST00000715766.1 link	n.1021+25330A>G	intron_variant	Intron 10 of 10

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

55061

AN:

151916

Hom.:

10056

Cov.:

show subpopulations

Gnomad AFR

AF:

0.389

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.366

Gnomad FIN

AF:

0.323

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.370

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

GnomAD4 genome

AF:

0.362

AC:

55082

AN:

152036

Hom.:

10056

Cov.:

AF XY:

0.360

AC XY:

26747

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.389

AC:

16105

AN:

41448

American (AMR)

AF:

0.302

AC:

4620

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.360

AC:

1247

AN:

3468

East Asian (EAS)

AF:

0.330

AC:

1704

AN:

5162

South Asian (SAS)

AF:

0.365

AC:

1763

AN:

4824

European-Finnish (FIN)

AF:

0.323

AC:

3408

AN:

10560

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.368

AC:

25009

AN:

67984

Other (OTH)

AF:

0.369

AC:

780

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1832

3664

5497

7329

9161

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

546

1092

1638

2184

2730

<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:

0.352

Hom.:

1304

Bravo

AF:

0.361

Asia WGS

AF:

0.383

AC:

1328

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.20

(source)

DANN

Benign

0.45

PhyloP100

-1.2

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