Genetic Variant LST1:c.19+35A>G (chr6-31587353-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 NM_205839.3(LST1):c.19+35A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 1,608,576 control chromosomes in the GnomAD database, including 287,829 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 0.60 ( 27269 hom., cov: 30)

Exomes 𝑓: 0.60 ( 260560 hom. )

Consequence

LST1
NM_205839.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.119

Publications

61 publications found

Variant links:

Genes affected

LST1 (HGNC:14189): (leukocyte specific transcript 1) The protein encoded by this gene is a membrane protein that can inhibit the proliferation of lymphocytes. Expression of this gene is enhanced by lipopolysaccharide, interferon-gamma, and bacteria. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

LST1 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_205839.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LST1	NM_205839.3	MANE Select	c.19+35A>G	intron	N/A	NP_995311.2	O00453-1
LST1	NM_007161.3		c.19+35A>G	intron	N/A	NP_009092.3	O00453-11
LST1	NM_001166538.1		c.19+35A>G	intron	N/A	NP_001160010.1	O00453-13

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LST1	ENST00000438075.7	TSL:1 MANE Select	c.19+35A>G	intron	N/A	ENSP00000391929.3	O00453-1
LST1	ENST00000376093.6	TSL:1	c.19+35A>G	intron	N/A	ENSP00000365261.2	O00453-11
LST1	ENST00000376086.7	TSL:1	c.19+35A>G	intron	N/A	ENSP00000365254.3	O00453-13

Frequencies

GnomAD3 genomes

AF:

0.598

AC:

90640

AN:

151668

Hom.:

27252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.646

Gnomad AMI

AF:

0.580

Gnomad AMR

AF:

0.534

Gnomad ASJ

AF:

0.526

Gnomad EAS

AF:

0.732

Gnomad SAS

AF:

0.712

Gnomad FIN

AF:

0.550

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.576

Gnomad OTH

AF:

0.580

GnomAD2 exomes

AF:

0.598

AC:

148809

AN:

248916

AF XY:

0.603

show subpopulations

Gnomad AFR exome

AF:

0.644

Gnomad AMR exome

AF:

0.506

Gnomad ASJ exome

AF:

0.534

Gnomad EAS exome

AF:

0.754

Gnomad FIN exome

AF:

0.549

Gnomad NFE exome

AF:

0.582

Gnomad OTH exome

AF:

0.574

GnomAD4 exome

AF:

0.595

AC:

867346

AN:

1456790

Hom.:

260560

Cov.:

AF XY:

0.598

AC XY:

433558

AN XY:

725040

show subpopulations

African (AFR)

AF:

0.648

AC:

21646

AN:

33380

American (AMR)

AF:

0.510

AC:

22807

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.536

AC:

14003

AN:

26106

East Asian (EAS)

AF:

0.707

AC:

28034

AN:

39680

South Asian (SAS)

AF:

0.704

AC:

60683

AN:

86168

European-Finnish (FIN)

AF:

0.557

AC:

29774

AN:

53416

Middle Eastern (MID)

AF:

0.545

AC:

3135

AN:

5750

European-Non Finnish (NFE)

AF:

0.588

AC:

651219

AN:

1107344

Other (OTH)

AF:

0.598

AC:

36045

AN:

60234

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

16832

33664

50495

67327

84159

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17972

35944

53916

71888

89860

<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:

0.598

AC:

90716

AN:

151786

Hom.:

27269

Cov.:

AF XY:

0.599

AC XY:

44382

AN XY:

74138

show subpopulations

African (AFR)

AF:

0.646

AC:

26718

AN:

41350

American (AMR)

AF:

0.535

AC:

8142

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.526

AC:

1823

AN:

3468

East Asian (EAS)

AF:

0.732

AC:

3778

AN:

5160

South Asian (SAS)

AF:

0.712

AC:

3429

AN:

4814

European-Finnish (FIN)

AF:

0.550

AC:

5790

AN:

10528

Middle Eastern (MID)

AF:

0.486

AC:

143

AN:

294

European-Non Finnish (NFE)

AF:

0.576

AC:

39143

AN:

67920

Other (OTH)

AF:

0.579

AC:

1223

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

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

760

1520

2280

3040

3800

<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:

0.577

Hom.:

43642

Bravo

AF:

0.594

Asia WGS

AF:

0.669

AC:

2327

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

9.0

(source)

DANN

Benign

0.60

PhyloP100

0.12

PromoterAI

0.018

Neutral

(source)

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over