Genetic Variant LINC01122:n.1043-53206C>T (chr2-59082913-C-T) – 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.1043-53206C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,160 control chromosomes in the GnomAD database, including 48,628 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 0.79 ( 48628 hom., cov: 32)

Consequence

LINC01122
ENST00000422723.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.269

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 (EAS) allele frequency at 95% confidence interval = 0.975 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.1043-53206C>T	intron_variant	Intron 9 of 10	3
LINC01122	ENST00000650010.2 link	n.1991+21063C>T	intron_variant	Intron 11 of 14
LINC01122	ENST00000715766.1 link	n.914-53206C>T	intron_variant	Intron 9 of 10

Frequencies

GnomAD3 genomes

AF:

0.792

AC:

120489

AN:

152042

Hom.:

48579

Cov.:

show subpopulations

Gnomad AFR

AF:

0.914

Gnomad AMI

AF:

0.581

Gnomad AMR

AF:

0.821

Gnomad ASJ

AF:

0.671

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.831

Gnomad FIN

AF:

0.755

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.710

Gnomad OTH

AF:

0.749

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

GnomAD4 genome

AF:

0.793

AC:

120594

AN:

152160

Hom.:

48628

Cov.:

AF XY:

0.796

AC XY:

59172

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.914

AC:

37983

AN:

41546

American (AMR)

AF:

0.821

AC:

12540

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.671

AC:

2328

AN:

3470

East Asian (EAS)

AF:

0.998

AC:

5155

AN:

5166

South Asian (SAS)

AF:

0.831

AC:

4000

AN:

4816

European-Finnish (FIN)

AF:

0.755

AC:

7991

AN:

10588

Middle Eastern (MID)

AF:

0.653

AC:

192

AN:

294

European-Non Finnish (NFE)

AF:

0.710

AC:

48295

AN:

67984

Other (OTH)

AF:

0.749

AC:

1581

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1249

2497

3746

4994

6243

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

866

1732

2598

3464

4330

<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:

0.757

Hom.:

17472

Bravo

AF:

0.803

Asia WGS

AF:

0.896

AC:

3115

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

0.15

(source)

DANN

Benign

0.56

PhyloP100

-0.27

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