rs1800683
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000595.4(LTA):c.-162G>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 0.368 in 234,314 control chromosomes in the GnomAD database, including 16,617 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 0.38 ( 11706 hom., cov: 33)
Exomes 𝑓: 0.34 ( 4911 hom. )
Consequence
LTA
NM_000595.4 5_prime_UTR
NM_000595.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.212
Genes affected
LTA (HGNC:6709): (lymphotoxin alpha) The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTA | NM_000595.4 | c.-162G>A | 5_prime_UTR_variant | 1/4 | ENST00000418386.3 | ||
LOC100287329 | NR_149045.1 | n.121+289C>T | intron_variant, non_coding_transcript_variant | ||||
LTA | NM_001159740.2 | c.-18G>A | 5_prime_UTR_variant | 1/4 | |||
LTA | XM_047418773.1 | c.-18G>A | 5_prime_UTR_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTA | ENST00000418386.3 | c.-162G>A | 5_prime_UTR_variant | 1/4 | 1 | NM_000595.4 | P1 | ||
ENST00000691266.1 | n.118+289C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.384 AC: 58285AN: 151930Hom.: 11693 Cov.: 33
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GnomAD4 exome AF: 0.338 AC: 27777AN: 82266Hom.: 4911 Cov.: 0 AF XY: 0.335 AC XY: 14380AN XY: 42892
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GnomAD4 genome ? AF: 0.384 AC: 58339AN: 152048Hom.: 11706 Cov.: 33 AF XY: 0.379 AC XY: 28197AN XY: 74326
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at