rs2256974

chr6-31587615-C-Achr6-31587615-C-T

Variant summary

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

The NM_205839.3(LST1):c.20-26C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,444,576 control chromosomes in the GnomAD database, including 29,160 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 0.24 (5077 hom., cov: 31)
  • Exomes 𝑓: 0.18 (24083 hom.)
• Consequence: LST1 NM_205839.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LST1	NM_205839.3	c.20-26C>A		intron_variant		ENST00000438075.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LST1	ENST00000438075.7	c.20-26C>A		intron_variant		1	NM_205839.3	P1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36687 AN: 151926 Hom.: 5073 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.225

GnomAD3 exomes AF: 0.216 AC: 40001 AN: 184772 Hom.: 4890 AF XY: 0.203 AC XY: 20297 AN XY: 99898

Gnomad AFR exome AF: 0.371

Gnomad AMR exome AF: 0.285

Gnomad ASJ exome AF: 0.178

Gnomad EAS exome AF: 0.407

Gnomad SAS exome AF: 0.122

Gnomad FIN exome AF: 0.175

Gnomad NFE exome AF: 0.174

Gnomad OTH exome AF: 0.206

GnomAD4 exome AF: 0.184 AC: 238102 AN: 1292532 Hom.: 24083 Cov.: 18 AF XY: 0.180 AC XY: 115801 AN XY: 642924

Gnomad4 AFR exome AF: 0.371

Gnomad4 AMR exome AF: 0.276

Gnomad4 ASJ exome AF: 0.180

Gnomad4 EAS exome AF: 0.389

Gnomad4 SAS exome AF: 0.117

Gnomad4 FIN exome AF: 0.184

Gnomad4 NFE exome AF: 0.172

Gnomad4 OTH exome AF: 0.196

GnomAD4 genome AF: 0.242 AC: 36729 AN: 152044 Hom.: 5077 Cov.: 31 AF XY: 0.242 AC XY: 17999 AN XY: 74312

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.224

Alfa AF: 0.185 Hom.: 2636

Bravo AF: 0.255

Asia WGS AF: 0.237 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.9
Dann	Benign	0.53

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: rs2256974; hg19: chr6-31555392;