1-54053434-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001305049.1(TMEM59):​c.-283C>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 0.000032 in 530,466 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000042 ( 0 hom. )

Consequence

TMEM59
NM_001305049.1 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.82
Variant links:
Genes affected
TMEM59 (HGNC:1239): (transmembrane protein 59) This gene encodes a protein shown to regulate autophagy in response to bacterial infection. This protein may also regulate the retention of amyloid precursor protein (APP) in the Golgi apparatus through its control of APP glycosylation. Overexpression of this protein has been found to promote apoptosis in a glioma cell line. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TMEM59NM_001305049.1 linkc.-283C>A 5_prime_UTR_variant Exon 1 of 8 NP_001291978.1 Q9BXS4
TMEM59NM_001305051.1 linkc.-283C>A 5_prime_UTR_variant Exon 1 of 8 NP_001291980.1 Q9BXS4Q5T6Z8
TMEM59NM_001305052.1 linkc.-177C>A 5_prime_UTR_variant Exon 1 of 7 NP_001291981.1 Q9BXS4Q5T6Z8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMEM59ENST00000371341.5 linkc.-283C>A 5_prime_UTR_variant Exon 1 of 8 2 ENSP00000360392.1 Q5T6Z8
TMEM59ENST00000440019.5 linkc.-177C>A 5_prime_UTR_variant Exon 1 of 6 2 ENSP00000399761.1 Q5T706
TMEM59ENST00000452421.5 linkc.-246C>A upstream_gene_variant 5 ENSP00000397772.1 Q5T704
TMEM59ENST00000420738.5 linkc.-316C>A upstream_gene_variant 3 ENSP00000413792.1 Q5T706

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152146
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000423
AC:
16
AN:
378202
Hom.:
0
Cov.:
4
AF XY:
0.0000660
AC XY:
13
AN XY:
196916
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000730
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000387
Gnomad4 SAS exome
AF:
0.0000867
Gnomad4 FIN exome
AF:
0.0000387
Gnomad4 NFE exome
AF:
0.0000390
Gnomad4 OTH exome
AF:
0.0000445
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152264
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.0
DANN
Benign
0.59

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

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

Other links and lift over

dbSNP: rs2236512; hg19: chr1-54519107; API