dbSNP rs7769073: LST1:c.-100-370T>A (chr6-31586830-T-A) – 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.-100-370T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 166,940 control chromosomes in the GnomAD database, including 348 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 0.056 ( 313 hom., cov: 31)

Exomes 𝑓: 0.047 ( 35 hom. )

Consequence

LST1
NM_205839.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.36

Publications

17 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 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.-100-370T>A	intron	N/A	NP_995311.2	O00453-1
LST1	NM_205837.3		c.-101+23T>A	intron	N/A	NP_995309.2	O00453-12
LST1	NM_205838.3		c.-100-370T>A	intron	N/A	NP_995310.2	O00453-10

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LST1	ENST00000438075.7	TSL:1 MANE Select	c.-100-370T>A	intron	N/A	ENSP00000391929.3	O00453-1
LST1	ENST00000339530.8	TSL:1	c.-101+23T>A	intron	N/A	ENSP00000339201.4	O00453-12
LST1	ENST00000464526.1	TSL:1	n.123-370T>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0559

AC:

8489

AN:

151950

Hom.:

314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0745

Gnomad AMI

AF:

0.0440

Gnomad AMR

AF:

0.0372

Gnomad ASJ

AF:

0.0271

Gnomad EAS

AF:

0.0397

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.0565

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0442

Gnomad OTH

AF:

0.0498

GnomAD4 exome

AF:

0.0471

AC:

701

AN:

14872

Hom.:

Cov.:

AF XY:

0.0551

AC XY:

448

AN XY:

8134

show subpopulations

African (AFR)

AF:

0.0788

AC:

AN:

368

American (AMR)

AF:

0.0196

AC:

AN:

1070

Ashkenazi Jewish (ASJ)

AF:

0.0194

AC:

AN:

412

East Asian (EAS)

AF:

0.0400

AC:

AN:

600

South Asian (SAS)

AF:

0.125

AC:

252

AN:

2024

European-Finnish (FIN)

AF:

0.0295

AC:

AN:

474

Middle Eastern (MID)

AF:

0.0893

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0344

AC:

313

AN:

9096

Other (OTH)

AF:

0.0453

AC:

AN:

772

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

128

160

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0559

AC:

8495

AN:

152068

Hom.:

313

Cov.:

AF XY:

0.0576

AC XY:

4282

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.0745

AC:

3090

AN:

41480

American (AMR)

AF:

0.0371

AC:

567

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0271

AC:

AN:

3470

East Asian (EAS)

AF:

0.0396

AC:

205

AN:

5172

South Asian (SAS)

AF:

0.161

AC:

775

AN:

4806

European-Finnish (FIN)

AF:

0.0565

AC:

598

AN:

10590

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0442

AC:

3004

AN:

67960

Other (OTH)

AF:

0.0512

AC:

108

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

396

791

1187

1582

1978

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<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:

0.0497

Hom.:

Bravo

AF:

0.0530

Asia WGS

AF:

0.137

AC:

474

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.020

(source)

DANN

Benign

0.73

PhyloP100

-2.4

PromoterAI

0.052

Neutral

(source)

Mutation Taster

=100/0

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