6-31588804-T-A

Position:

• chr6-31588804-T-A

Variant summary

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

The NM_205839.3(LST1):​c.*128T>A variant causes a 3 prime UTR 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 NM_205839.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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=-0.88).
• 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/exons	MANE	Protein	UniProt
LST1	NM_205839.3	c.*128T>A		3_prime_UTR_variant	5/5	ENST00000438075.7	NP_995311.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LST1	ENST00000438075.7	c.*128T>A		3_prime_UTR_variant	5/5	1	NM_205839.3	ENSP00000391929	P1

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

Gnomad4 AFR exome AF: 0.228

Gnomad4 AMR exome AF: 0.202

Gnomad4 ASJ exome AF: 0.368

Gnomad4 EAS exome AF: 0.261

Gnomad4 SAS exome AF: 0.559

Gnomad4 FIN exome AF: 0.255

Gnomad4 NFE exome AF: 0.269

Gnomad4 OTH exome AF: 0.301

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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.301

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

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: rs1052248; hg19: chr6-31556581; COSMIC: COSV53002230; COSMIC: COSV53002230;