rs7769073

Variant names:

• chr6-31586830-T-A
• rs7769073
• NM_205839.3:c.-100-370T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 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=-0.88).
• 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 rank	MANE	Protein	UniProt
LST1	NM_205839.3	c.-100-370T>A		intron_variant	Intron 1 of 4	ENST00000438075.7	NP_995311.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LST1	ENST00000438075.7	c.-100-370T>A		intron_variant	Intron 1 of 4	1	NM_205839.3	ENSP00000391929.3

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

African (AFR) AF: 0.0788 AC: 29 AN: 368

American (AMR) AF: 0.0196 AC: 21 AN: 1070

Ashkenazi Jewish (ASJ) AF: 0.0194 AC: 8 AN: 412

East Asian (EAS) AF: 0.0400 AC: 24 AN: 600

South Asian (SAS) AF: 0.125 AC: 252 AN: 2024

European-Finnish (FIN) AF: 0.0295 AC: 14 AN: 474

Middle Eastern (MID) AF: 0.0893 AC: 5 AN: 56

European-Non Finnish (NFE) AF: 0.0344 AC: 313 AN: 9096

Other (OTH) AF: 0.0453 AC: 35 AN: 772

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

African (AFR) AF: 0.0745 AC: 3090 AN: 41480

American (AMR) AF: 0.0371 AC: 567 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3470

East Asian (EAS) AF: 0.0396 AC: 205 AN: 5172

South Asian (SAS) AF: 0.161 AC: 775 AN: 4806

European-Finnish (FIN) AF: 0.0565 AC: 598 AN: 10590

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3004 AN: 67960

Other (OTH) AF: 0.0512 AC: 108 AN: 2110

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
PhyloP100		-2.4
PromoterAI		0.052	Neutral
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: rs7769073; hg19: chr6-31554607;