rs2256965

Positions:

• chr6-31587353-A-G
• chr6-31587353-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LST1	NM_205839.3	c.19+35A>G		intron_variant		ENST00000438075.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LST1	ENST00000438075.7	c.19+35A>G		intron_variant		1	NM_205839.3	P1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90640 AN: 151668 Hom.: 27252 Cov.: 30

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

GnomAD3 exomes AF: 0.598 AC: 148809 AN: 248916 Hom.: 45354 AF XY: 0.603 AC XY: 81237 AN XY: 134738

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 SAS exome AF: 0.700

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.: 34 AF XY: 0.598 AC XY: 433558 AN XY: 725040

Gnomad4 AFR exome AF: 0.648

Gnomad4 AMR exome AF: 0.510

Gnomad4 ASJ exome AF: 0.536

Gnomad4 EAS exome AF: 0.707

Gnomad4 SAS exome AF: 0.704

Gnomad4 FIN exome AF: 0.557

Gnomad4 NFE exome AF: 0.588

Gnomad4 OTH exome AF: 0.598

GnomAD4 genome AF: 0.598 AC: 90716 AN: 151786 Hom.: 27269 Cov.: 30 AF XY: 0.599 AC XY: 44382 AN XY: 74138

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.579

Alfa AF: 0.573 Hom.: 30103

Bravo AF: 0.594

Asia WGS AF: 0.669 AC: 2327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.0
DANN	Benign	0.60

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

Other links and lift over

dbSNP: rs2256965; hg19: chr6-31555130; COSMIC: COSV53001239; COSMIC: COSV53001239;