rs1052248

Variant names:

• chr6-31588804-T-A
• rs1052248
• ENST00000464526.1:n.1727T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31588804-T-A
• chr6-31588804-T-C

Variant summary

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

The ENST00000464526.1(LST1):​n.1727T>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 0.287 in 1,101,512 control chromosomes in the GnomAD database, including 49,257 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 0.26 (5572 hom., cov: 32)
  • Exomes 𝑓: 0.29 (43685 hom.)
• Consequence: LST1 ENST00000464526.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 47 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LST1	NM_205839.3	c.*128T>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000438075.7	NP_995311.2
NCR3	NM_147130.3	c.*263A>T		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.*128T>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_205839.3	ENSP00000391929.3
NCR3	ENST00000340027.10	c.*263A>T		downstream_gene_variant		1	NM_147130.3	ENSP00000342156.5

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40122 AN: 152046 Hom.: 5560 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.291 AC: 276195 AN: 949348 Hom.: 43685 Cov.: 13 AF XY: 0.304 AC XY: 147695 AN XY: 485788

African (AFR) AF: 0.228 AC: 5223 AN: 22918

American (AMR) AF: 0.202 AC: 7530 AN: 37226

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 7785 AN: 21142

East Asian (EAS) AF: 0.261 AC: 9466 AN: 36300

South Asian (SAS) AF: 0.559 AC: 40339 AN: 72128

European-Finnish (FIN) AF: 0.255 AC: 12974 AN: 50968

Middle Eastern (MID) AF: 0.401 AC: 1879 AN: 4680

European-Non Finnish (NFE) AF: 0.269 AC: 178118 AN: 661214

Other (OTH) AF: 0.301 AC: 12881 AN: 42772

GnomAD4 genome AF: 0.264 AC: 40172 AN: 152164 Hom.: 5572 Cov.: 32 AF XY: 0.269 AC XY: 19979 AN XY: 74376

African (AFR) AF: 0.225 AC: 9354 AN: 41522

American (AMR) AF: 0.230 AC: 3519 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1237 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1305 AN: 5180

South Asian (SAS) AF: 0.547 AC: 2639 AN: 4824

European-Finnish (FIN) AF: 0.255 AC: 2701 AN: 10576

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18451 AN: 67984

Other (OTH) AF: 0.301 AC: 637 AN: 2116

Alfa AF: 0.262 Hom.: 806

Bravo AF: 0.256

Asia WGS AF: 0.385 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.81
PhyloP100		-0.037
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: rs1052248; hg19: chr6-31556581; COSMIC: COSV53002230; COSMIC: COSV53002230;