6-31587353-A-G

Variant names:

• chr6-31587353-A-G
• rs2256965
• ENST00000464526.1:n.276A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000464526.1(LST1):​n.276A>G variant causes a non coding transcript exon 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 ENST00000464526.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 61 publications found

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

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: ENST00000464526.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LST1	ENST00000464526.1	TSL:1	n.276A>G		non_coding_transcript_exon	Exon 2 of 2
	LST1	ENST00000438075.7	TSL:1 MANE Select	c.19+35A>G		intron	N/A	ENSP00000391929.3
	LST1	ENST00000376093.6	TSL:1	c.19+35A>G		intron	N/A	ENSP00000365261.2

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

GnomAD2 exomes AF: 0.598 AC: 148809 AN: 248916 AF XY: 0.603

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

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

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

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

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
DANN	Benign	0.60
PhyloP100		0.12
PromoterAI		0.018	Neutral
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

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