chr6-31587615-C-A

Variant names:

• chr6-31587615-C-A
• rs2256974
• ENST00000464526.1:n.538C>A

Variant summary

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

The ENST00000464526.1(LST1):​n.538C>A 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 0.19 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 ENST00000464526.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 52 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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.20-26C>A		intron	N/A	NP_995311.2
	LST1	NM_007161.3		c.20-26C>A		intron	N/A	NP_009092.3
	LST1	NM_001166538.1		c.19+297C>A		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.538C>A		non_coding_transcript_exon	Exon 2 of 2
	LST1	ENST00000438075.7	TSL:1 MANE Select	c.20-26C>A		intron	N/A	ENSP00000391929.3
	LST1	ENST00000376093.6	TSL:1	c.20-26C>A		intron	N/A	ENSP00000365261.2

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

GnomAD2 exomes AF: 0.216 AC: 40001 AN: 184772 AF XY: 0.203

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 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

African (AFR) AF: 0.371 AC: 11097 AN: 29942

American (AMR) AF: 0.276 AC: 10275 AN: 37210

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 4116 AN: 22840

East Asian (EAS) AF: 0.389 AC: 14730 AN: 37826

South Asian (SAS) AF: 0.117 AC: 8988 AN: 76972

European-Finnish (FIN) AF: 0.184 AC: 8760 AN: 47710

Middle Eastern (MID) AF: 0.179 AC: 955 AN: 5332

European-Non Finnish (NFE) AF: 0.172 AC: 168582 AN: 980618

Other (OTH) AF: 0.196 AC: 10599 AN: 54082

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

African (AFR) AF: 0.367 AC: 15197 AN: 41442

American (AMR) AF: 0.262 AC: 4007 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 602 AN: 3464

East Asian (EAS) AF: 0.403 AC: 2077 AN: 5148

South Asian (SAS) AF: 0.136 AC: 656 AN: 4830

European-Finnish (FIN) AF: 0.176 AC: 1863 AN: 10594

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11656 AN: 67966

Other (OTH) AF: 0.224 AC: 473 AN: 2110

Alfa AF: 0.197 Hom.: 9993

Bravo AF: 0.255

Asia WGS AF: 0.237 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.9
DANN	Benign	0.53
PhyloP100		-0.15
PromoterAI		0.0062	Neutral
Mutation Taster		=100/0	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: rs2256974; hg19: chr6-31555392;