chr13-111320927-C-A

Variant summary

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

The NM_152324.3(TEX29):​c.37C>A​(p.His13Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,611,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000044 ( 0 hom. )

Consequence

TEX29
NM_152324.3 missense

Scores

1
3
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.60
Variant links:
Genes affected
TEX29 (HGNC:20370): (testis expressed 29) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (MetaRNN=0.028852582).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TEX29NM_152324.3 linkuse as main transcriptc.37C>A p.His13Asn missense_variant 2/6 ENST00000283547.2 NP_689537.1
TEX29XM_017020387.2 linkuse as main transcriptc.118C>A p.His40Asn missense_variant 2/6 XP_016875876.2
TEX29NM_001303133.1 linkuse as main transcriptc.-40C>A 5_prime_UTR_variant 2/7 NP_001290062.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TEX29ENST00000283547.2 linkuse as main transcriptc.37C>A p.His13Asn missense_variant 2/61 NM_152324.3 ENSP00000283547 P1
TEX29ENST00000497241.5 linkuse as main transcriptc.118C>A p.His40Asn missense_variant, NMD_transcript_variant 2/75 ENSP00000431661

Frequencies

GnomAD3 genomes
AF:
0.0000332
AC:
5
AN:
150822
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00144
Gnomad EAS
AF:
0.00
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
GnomAD3 exomes
AF:
0.000104
AC:
26
AN:
250564
Hom.:
0
AF XY:
0.000133
AC XY:
18
AN XY:
135622
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00229
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000885
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000438
AC:
64
AN:
1461132
Hom.:
0
Cov.:
34
AF XY:
0.0000509
AC XY:
37
AN XY:
726864
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00168
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000899
Gnomad4 OTH exome
AF:
0.0000828
GnomAD4 genome
AF:
0.0000332
AC:
5
AN:
150822
Hom.:
0
Cov.:
30
AF XY:
0.0000408
AC XY:
3
AN XY:
73558
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00144
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
Alfa
AF:
0.000230
Hom.:
0
Bravo
AF:
0.0000416
ExAC
AF:
0.000115
AC:
14

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsFeb 06, 2023The c.37C>A (p.H13N) alteration is located in exon 2 (coding exon 1) of the TEX29 gene. This alteration results from a C to A substitution at nucleotide position 37, causing the histidine (H) at amino acid position 13 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.56
CADD
Benign
14
DANN
Benign
0.76
DEOGEN2
Benign
0.23
T
Eigen
Benign
-0.99
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.068
N
LIST_S2
Benign
0.42
T
M_CAP
Benign
0.0018
T
MetaRNN
Benign
0.029
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.81
L
MutationTaster
Benign
1.0
N
PrimateAI
Uncertain
0.51
T
PROVEAN
Pathogenic
-4.9
D
REVEL
Benign
0.025
Sift
Uncertain
0.020
D
Sift4G
Uncertain
0.029
D
Polyphen
0.23
B
Vest4
0.44
MutPred
0.22
Loss of ubiquitination at K8 (P = 0.1037);
MVP
0.048
MPC
0.33
ClinPred
0.071
T
GERP RS
1.6
Varity_R
0.24
gMVP
0.13

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: rs201674534; hg19: chr13-111973274; API