rs1799964

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000595.4(LTA):​c.*838T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,164 control chromosomes in the GnomAD database, including 2,988 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 0.20 ( 2988 hom., cov: 30)

Consequence

LTA
NM_000595.4 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13
Variant links:
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=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LTANM_000595.4 linkc.*838T>C downstream_gene_variant ENST00000418386.3 NP_000586.2 P01374Q5STV3
LTANM_001159740.2 linkc.*838T>C downstream_gene_variant NP_001153212.1 P01374Q5STV3
LTAXM_047418773.1 linkc.*838T>C downstream_gene_variant XP_047274729.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LTAENST00000418386.3 linkc.*838T>C downstream_gene_variant 1 NM_000595.4 ENSP00000413450.2 P01374
LTAENST00000454783.5 linkc.*838T>C downstream_gene_variant 2 ENSP00000403495.1 P01374
LTAENST00000471842.1 linkn.*207T>C downstream_gene_variant 2
LTAENST00000489638.5 linkn.*207T>C downstream_gene_variant 5

Frequencies

GnomAD3 genomes
AF:
0.196
AC:
29605
AN:
151046
Hom.:
2988
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.184
Gnomad AMR
AF:
0.193
Gnomad ASJ
AF:
0.219
Gnomad EAS
AF:
0.191
Gnomad SAS
AF:
0.326
Gnomad FIN
AF:
0.178
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.209
Gnomad OTH
AF:
0.236
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.196
AC:
29631
AN:
151164
Hom.:
2988
Cov.:
30
AF XY:
0.197
AC XY:
14541
AN XY:
73770
show subpopulations
Gnomad4 AFR
AF:
0.162
Gnomad4 AMR
AF:
0.193
Gnomad4 ASJ
AF:
0.219
Gnomad4 EAS
AF:
0.191
Gnomad4 SAS
AF:
0.324
Gnomad4 FIN
AF:
0.178
Gnomad4 NFE
AF:
0.209
Gnomad4 OTH
AF:
0.236
Alfa
AF:
0.211
Hom.:
5947
Bravo
AF:
0.194
Asia WGS
AF:
0.275
AC:
954
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
4.6
DANN
Benign
0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1799964; hg19: chr6-31542308; API