6-31586830-T-A

Position:

• chr6-31586830-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.-100-370T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 166,940 control chromosomes in the GnomAD database, including 348 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 0.056 (313 hom., cov: 31)
  • Exomes 𝑓: 0.047 (35 hom.)
• Consequence: LST1 NM_205839.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

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 = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LST1	NM_205839.3	c.-100-370T>A		intron_variant		ENST00000438075.7	NP_995311.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LST1	ENST00000438075.7	c.-100-370T>A		intron_variant		1	NM_205839.3	ENSP00000391929	P1

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8489 AN: 151950 Hom.: 314 Cov.: 31

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0565

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0498

GnomAD4 exome AF: 0.0471 AC: 701 AN: 14872 Hom.: 35 Cov.: 0 AF XY: 0.0551 AC XY: 448 AN XY: 8134

Gnomad4 AFR exome AF: 0.0788

Gnomad4 AMR exome AF: 0.0196

Gnomad4 ASJ exome AF: 0.0194

Gnomad4 EAS exome AF: 0.0400

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.0295

Gnomad4 NFE exome AF: 0.0344

Gnomad4 OTH exome AF: 0.0453

GnomAD4 genome AF: 0.0559 AC: 8495 AN: 152068 Hom.: 313 Cov.: 31 AF XY: 0.0576 AC XY: 4282 AN XY: 74346

Gnomad4 AFR AF: 0.0745

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.0396

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0565

Gnomad4 NFE AF: 0.0442

Gnomad4 OTH AF: 0.0512

Alfa AF: 0.0497 Hom.: 31

Bravo AF: 0.0530

Asia WGS AF: 0.137 AC: 474 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	0.020
DANN	Benign	0.73

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: rs7769073; hg19: chr6-31554607;