rs1058007

Variant summary

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

The NM_021156.4(TMX4):​c.*770G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,924 control chromosomes in the GnomAD database, including 9,242 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 0.25 ( 9242 hom., cov: 32)
Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

TMX4
NM_021156.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.42
Variant links:
Genes affected
TMX4 (HGNC:25237): (thioredoxin related transmembrane protein 4) This gene encodes a member of the disulfide isomerase (PDI) family of endoplasmic reticulum (ER) proteins that catalyze protein folding and thiol-disulfide interchange reactions. The encoded protein has an N-terminal ER-signal sequence, a catalytically active thioredoxin domain, one transmembrane domain and C-terminal ASP/GLU-rich calcium binding domain. Unlike most members of this gene family, it lacks a C-terminal ER-retention sequence. The encoded protein has been shown to have reductase activity in vitro. [provided by RefSeq, Jan 2017]

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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=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TMX4NM_021156.4 linkuse as main transcriptc.*770G>A 3_prime_UTR_variant 8/8 ENST00000246024.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TMX4ENST00000246024.7 linkuse as main transcriptc.*770G>A 3_prime_UTR_variant 8/81 NM_021156.4 P1

Frequencies

GnomAD3 genomes
AF:
0.254
AC:
38578
AN:
151804
Hom.:
9216
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.603
Gnomad AMI
AF:
0.0329
Gnomad AMR
AF:
0.223
Gnomad ASJ
AF:
0.119
Gnomad EAS
AF:
0.592
Gnomad SAS
AF:
0.102
Gnomad FIN
AF:
0.0978
Gnomad MID
AF:
0.121
Gnomad NFE
AF:
0.0692
Gnomad OTH
AF:
0.244
GnomAD4 exome
AF:
0.500
AC:
1
AN:
2
Hom.:
0
Cov.:
0
AF XY:
0.500
AC XY:
1
AN XY:
2
show subpopulations
Gnomad4 AFR exome
AF:
0.500
GnomAD4 genome
AF:
0.254
AC:
38651
AN:
151922
Hom.:
9242
Cov.:
32
AF XY:
0.254
AC XY:
18820
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.603
Gnomad4 AMR
AF:
0.223
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.591
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.0978
Gnomad4 NFE
AF:
0.0692
Gnomad4 OTH
AF:
0.243
Alfa
AF:
0.120
Hom.:
2288
Bravo
AF:
0.286
Asia WGS
AF:
0.337
AC:
1172
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
5.2
DANN
Benign
0.62

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: rs1058007; hg19: chr20-7962128; API