chr6-31586159-G-A

Variant names:

• chr6-31586159-G-A
• rs17200775
• ENST00000418507.6:c.-257G>A

Variant summary

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

The ENST00000418507.6(LST1):​c.-257G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 152,204 control chromosomes in the GnomAD database, including 117 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 0.035 (117 hom., cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LST1 ENST00000418507.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418507.6. 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.-257G>A		upstream_gene	N/A	NP_995311.2
	LST1	NM_205838.3		c.-257G>A		upstream_gene	N/A	NP_995310.2
	LST1	NR_029461.2		n.-118G>A		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LST1	ENST00000418507.6	TSL:2	c.-257G>A		5_prime_UTR	Exon 1 of 4	ENSP00000405900.2
	LST1	ENST00000438075.7	TSL:1 MANE Select	c.-257G>A		upstream_gene	N/A	ENSP00000391929.3
	LST1	ENST00000464526.1	TSL:1	n.-35G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0345 AC: 5241 AN: 152086 Hom.: 117 Cov.: 30

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0373

Gnomad ASJ AF: 0.0743

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.00631

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0445

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 10

GnomAD4 genome AF: 0.0346 AC: 5261 AN: 152204 Hom.: 117 Cov.: 30 AF XY: 0.0333 AC XY: 2475 AN XY: 74406

African (AFR) AF: 0.0527 AC: 2190 AN: 41522

American (AMR) AF: 0.0372 AC: 569 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0743 AC: 258 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5174

South Asian (SAS) AF: 0.0216 AC: 104 AN: 4814

European-Finnish (FIN) AF: 0.00631 AC: 67 AN: 10616

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0280 AC: 1904 AN: 68002

Other (OTH) AF: 0.0440 AC: 93 AN: 2114

Alfa AF: 0.0258 Hom.: 151

Bravo AF: 0.0384

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.41
PhyloP100		-1.2
PromoterAI		-0.13	Neutral
Mutation Taster		=300/0	polymorphism

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: rs17200775; hg19: chr6-31553936;