Variant rs1052248 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_205839.3(LST1):c.*128T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,101,512 control chromosomes in the GnomAD database, including 49,257 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 0.26 ( 5572 hom., cov: 32)

Exomes 𝑓: 0.29 ( 43685 hom. )

Consequence

LST1
NM_205839.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0370

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LST1	NM_205839.3 linkuse as main transcript	c.*128T>A		3_prime_UTR_variant	5/5	ENST00000438075.7	NP_995311.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LST1	ENST00000438075.7 linkuse as main transcript	c.*128T>A		3_prime_UTR_variant	5/5	1	NM_205839.3	ENSP00000391929	P1	O00453-1

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40122

AN:

152046

Hom.:

5560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.253

Gnomad SAS

AF:

0.547

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.301

GnomAD4 exome

AF:

0.291

AC:

276195

AN:

949348

Hom.:

43685

Cov.:

AF XY:

0.304

AC XY:

147695

AN XY:

485788

show subpopulations

Gnomad4 AFR exome

AF:

0.228

Gnomad4 AMR exome

AF:

0.202

Gnomad4 ASJ exome

AF:

0.368

Gnomad4 EAS exome

AF:

0.261

Gnomad4 SAS exome

AF:

0.559

Gnomad4 FIN exome

AF:

0.255

Gnomad4 NFE exome

AF:

0.269

Gnomad4 OTH exome

AF:

0.301

GnomAD4 genome

AF:

0.264

AC:

40172

AN:

152164

Hom.:

5572

Cov.:

AF XY:

0.269

AC XY:

19979

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.225

Gnomad4 AMR

AF:

0.230

Gnomad4 ASJ

AF:

0.356

Gnomad4 EAS

AF:

0.252

Gnomad4 SAS

AF:

0.547

Gnomad4 FIN

AF:

0.255

Gnomad4 NFE

AF:

0.271

Gnomad4 OTH

AF:

0.301

Alfa

AF:

0.262

Hom.:

806

Bravo

AF:

0.256

Asia WGS

AF:

0.385

AC:

1336

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.7

DANN

Benign

0.81

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over