Genetic Variant LIAT1:n.*239-2338T>C (chr17-421142-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 ENST00000575151.1(LIAT1):n.*239-2338T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 189,628 control chromosomes in the GnomAD database, including 17,041 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 0.42 ( 14905 hom., cov: 32)

Exomes 𝑓: 0.33 ( 2136 hom. )

Consequence

LIAT1
ENST00000575151.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.581

Publications

31 publications found

Variant links:

COSMIC-nc: COSV73844534

Genes affected

LIAT1 (HGNC:33800): (ligand of ATE1) Predicted to be involved in protein arginylation. [provided by Alliance of Genome Resources, Apr 2022]

LIAT1 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 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	Protein
LIAT1	ENST00000575151.1 link	n.*239-2338T>C	intron_variant	Intron 1 of 1	3	ENSP00000466848.1
LIAT1	ENST00000629953.1 link	n.440+192T>C	intron_variant	Intron 2 of 4	5
LIAT1	ENST00000571106.1 link	c.*313T>C	downstream_gene_variant		2	ENSP00000458320.1

Frequencies

GnomAD3 genomes

AF:

0.417

AC:

63403

AN:

151936

Hom.:

14876

Cov.:

show subpopulations

Gnomad AFR

AF:

0.630

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.384

Gnomad ASJ

AF:

0.461

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.500

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.390

GnomAD4 exome

AF:

0.329

AC:

12371

AN:

37574

Hom.:

2136

Cov.:

AF XY:

0.327

AC XY:

6257

AN XY:

19128

show subpopulations

African (AFR)

AF:

0.618

AC:

901

AN:

1458

American (AMR)

AF:

0.373

AC:

395

AN:

1060

Ashkenazi Jewish (ASJ)

AF:

0.449

AC:

716

AN:

1596

East Asian (EAS)

AF:

0.519

AC:

1440

AN:

2772

South Asian (SAS)

AF:

0.462

AC:

146

AN:

316

European-Finnish (FIN)

AF:

0.271

AC:

548

AN:

2020

Middle Eastern (MID)

AF:

0.447

AC:

AN:

206

European-Non Finnish (NFE)

AF:

0.283

AC:

7212

AN:

25450

Other (OTH)

AF:

0.342

AC:

921

AN:

2696

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

400

799

1199

1598

1998

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

162

216

270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.417

AC:

63481

AN:

152054

Hom.:

14905

Cov.:

AF XY:

0.418

AC XY:

31062

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.630

AC:

26130

AN:

41482

American (AMR)

AF:

0.384

AC:

5864

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.461

AC:

1600

AN:

3472

East Asian (EAS)

AF:

0.543

AC:

2806

AN:

5166

South Asian (SAS)

AF:

0.498

AC:

2404

AN:

4824

European-Finnish (FIN)

AF:

0.296

AC:

3125

AN:

10568

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.298

AC:

20285

AN:

67970

Other (OTH)

AF:

0.388

AC:

820

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1759

3519

5278

7038

8797

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

574

1148

1722

2296

2870

<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:

0.336

Hom.:

37221

Bravo

AF:

0.435

Asia WGS

AF:

0.493

AC:

1716

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.13

(source)

DANN

Benign

0.43

PhyloP100

-0.58

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over