rs3087617

Variant names:

• chr6-31588879-A-T
• rs3087617
• ENST00000464526.1:n.1802A>T

Variant summary

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

The ENST00000464526.1(LST1):​n.1802A>T 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 0.0884 in 874,382 control chromosomes in the GnomAD database, including 3,990 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 0.073 (499 hom., cov: 32)
  • Exomes 𝑓: 0.092 (3491 hom.)
• Consequence: LST1 ENST00000464526.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 9 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]

NCR3 (HGNC:19077): (natural cytotoxicity triggering receptor 3) The protein encoded by this gene is a natural cytotoxicity receptor (NCR) that may aid NK cells in the lysis of tumor cells. The encoded protein interacts with CD3-zeta (CD247), a T-cell receptor. A single nucleotide polymorphism in the 5' untranslated region of this gene has been associated with mild malaria suceptibility. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LST1	NM_205839.3	c.*203A>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000438075.7	NP_995311.2
NCR3	NM_147130.3	c.*188T>A		downstream_gene_variant		ENST00000340027.10	NP_667341.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LST1	ENST00000438075.7	c.*203A>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_205839.3	ENSP00000391929.3
NCR3	ENST00000340027.10	c.*188T>A		downstream_gene_variant		1	NM_147130.3	ENSP00000342156.5

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11065 AN: 152000 Hom.: 500 Cov.: 32

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0872

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0831

Gnomad OTH AF: 0.0704

GnomAD4 exome AF: 0.0917 AC: 66201 AN: 722264 Hom.: 3491 Cov.: 9 AF XY: 0.0950 AC XY: 34754 AN XY: 365692

African (AFR) AF: 0.0346 AC: 597 AN: 17240

American (AMR) AF: 0.0516 AC: 978 AN: 18942

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 2148 AN: 15396

East Asian (EAS) AF: 0.145 AC: 4652 AN: 32122

South Asian (SAS) AF: 0.181 AC: 8679 AN: 47936

European-Finnish (FIN) AF: 0.0818 AC: 3604 AN: 44084

Middle Eastern (MID) AF: 0.128 AC: 349 AN: 2718

European-Non Finnish (NFE) AF: 0.0826 AC: 42026 AN: 509020

Other (OTH) AF: 0.0910 AC: 3168 AN: 34806

GnomAD4 genome AF: 0.0728 AC: 11073 AN: 152118 Hom.: 499 Cov.: 32 AF XY: 0.0763 AC XY: 5674 AN XY: 74366

African (AFR) AF: 0.0353 AC: 1464 AN: 41494

American (AMR) AF: 0.0497 AC: 759 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.121 AC: 623 AN: 5168

South Asian (SAS) AF: 0.176 AC: 849 AN: 4814

European-Finnish (FIN) AF: 0.0872 AC: 925 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0831 AC: 5648 AN: 67984

Other (OTH) AF: 0.0701 AC: 148 AN: 2110

Alfa AF: 0.0766 Hom.: 59

Bravo AF: 0.0655

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.071
PhyloP100		-0.35
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: rs3087617; hg19: chr6-31556656; COSMIC: COSV107227936; COSMIC: COSV107227936;