chr14-105411377-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001195082.2(TEX22):​c.160C>T​(p.Pro54Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000085 in 1,175,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P54A) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 8.5e-7 ( 0 hom. )

Consequence

TEX22
NM_001195082.2 missense

Scores

4
2
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.578
Variant links:
Genes affected
TEX22 (HGNC:40026): (testis expressed 22) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.15730429).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TEX22NM_001195082.2 linkc.160C>T p.Pro54Ser missense_variant Exon 3 of 4 ENST00000451127.3 NP_001182011.1 C9J3V5
TEX22XM_006720234.4 linkc.160C>T p.Pro54Ser missense_variant Exon 3 of 4 XP_006720297.1 C9J3V5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TEX22ENST00000451127.3 linkc.160C>T p.Pro54Ser missense_variant Exon 3 of 4 2 NM_001195082.2 ENSP00000397002.2 C9J3V5
TEX22ENST00000548638.5 linkn.150+11887C>T intron_variant Intron 2 of 5 5 ENSP00000449736.1 F8VX47

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
8.50e-7
AC:
1
AN:
1175946
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
573334
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000103
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Benign
-0.042
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.12
T
Eigen
Benign
-0.50
Eigen_PC
Benign
-0.53
FATHMM_MKL
Benign
0.40
N
LIST_S2
Benign
0.53
T
M_CAP
Pathogenic
0.60
D
MetaRNN
Benign
0.16
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.69
N
PrimateAI
Uncertain
0.60
T
PROVEAN
Pathogenic
-8.0
D
REVEL
Benign
0.12
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.31
B
Vest4
0.25
MutPred
0.19
Loss of glycosylation at P54 (P = 0.0286);
MVP
0.061
ClinPred
0.91
D
GERP RS
1.8
Varity_R
0.55
gMVP
0.031

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-105877714; API