1-54053434-G-C

Variant summary

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

The NM_001305049.1(TMEM59):​c.-283C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 530,254 control chromosomes in the GnomAD database, including 2,927 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 0.055 ( 738 hom., cov: 32)
Exomes 𝑓: 0.051 ( 2189 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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TMEM59NM_001305049.1 linkc.-283C>G 5_prime_UTR_variant Exon 1 of 8 NP_001291978.1 Q9BXS4
TMEM59NM_001305051.1 linkc.-283C>G 5_prime_UTR_variant Exon 1 of 8 NP_001291980.1 Q9BXS4Q5T6Z8
TMEM59NM_001305052.1 linkc.-177C>G 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>G 5_prime_UTR_variant Exon 1 of 8 2 ENSP00000360392.1 Q5T6Z8
TMEM59ENST00000440019.5 linkc.-177C>G 5_prime_UTR_variant Exon 1 of 6 2 ENSP00000399761.1 Q5T706
TMEM59ENST00000452421.5 linkc.-246C>G upstream_gene_variant 5 ENSP00000397772.1 Q5T704
TMEM59ENST00000420738.5 linkc.-316C>G upstream_gene_variant 3 ENSP00000413792.1 Q5T706

Frequencies

GnomAD3 genomes
AF:
0.0544
AC:
8271
AN:
152140
Hom.:
727
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0416
Gnomad AMI
AF:
0.0230
Gnomad AMR
AF:
0.198
Gnomad ASJ
AF:
0.0242
Gnomad EAS
AF:
0.330
Gnomad SAS
AF:
0.0401
Gnomad FIN
AF:
0.0434
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0135
Gnomad OTH
AF:
0.0636
GnomAD4 exome
AF:
0.0509
AC:
19255
AN:
377996
Hom.:
2189
Cov.:
4
AF XY:
0.0489
AC XY:
9618
AN XY:
196818
show subpopulations
Gnomad4 AFR exome
AF:
0.0392
Gnomad4 AMR exome
AF:
0.242
Gnomad4 ASJ exome
AF:
0.0245
Gnomad4 EAS exome
AF:
0.349
Gnomad4 SAS exome
AF:
0.0277
Gnomad4 FIN exome
AF:
0.0436
Gnomad4 NFE exome
AF:
0.0130
Gnomad4 OTH exome
AF:
0.0501
GnomAD4 genome
AF:
0.0545
AC:
8301
AN:
152258
Hom.:
738
Cov.:
32
AF XY:
0.0589
AC XY:
4382
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0417
Gnomad4 AMR
AF:
0.199
Gnomad4 ASJ
AF:
0.0242
Gnomad4 EAS
AF:
0.330
Gnomad4 SAS
AF:
0.0400
Gnomad4 FIN
AF:
0.0434
Gnomad4 NFE
AF:
0.0135
Gnomad4 OTH
AF:
0.0653
Alfa
AF:
0.00675
Hom.:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.1
DANN
Benign
0.42

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