X-54440443-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_058163.3(TSR2):​c.22G>C​(p.Ala8Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,127,308 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 54 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.000098 ( 0 hom., 5 hem., cov: 23)
Exomes 𝑓: 0.00019 ( 0 hom. 49 hem. )

Consequence

TSR2
NM_058163.3 missense

Scores

1
16

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: -0.653
Variant links:
Genes affected
TSR2 (HGNC:25455): (TSR2 ribosome maturation factor) The protein encoded by this gene appears to repress the transcription of NF-kappaB and may be involved in apoptosis. Defects in this gene are a cause of Diamond-Blackfan anemia. [provided by RefSeq, Oct 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.04404813).
BS2
High Hemizygotes in GnomAd4 at 5 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TSR2NM_058163.3 linkc.22G>C p.Ala8Pro missense_variant Exon 1 of 5 ENST00000375151.5 NP_477511.1 Q969E8A0A024R9U9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TSR2ENST00000375151.5 linkc.22G>C p.Ala8Pro missense_variant Exon 1 of 5 1 NM_058163.3 ENSP00000364293.4 Q969E8

Frequencies

GnomAD3 genomes
AF:
0.0000978
AC:
11
AN:
112508
Hom.:
0
Cov.:
23
AF XY:
0.000144
AC XY:
5
AN XY:
34640
show subpopulations
Gnomad AFR
AF:
0.0000323
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000940
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000169
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000470
AC:
4
AN:
85108
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
14726
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000103
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000194
AC:
197
AN:
1014800
Hom.:
0
Cov.:
30
AF XY:
0.000153
AC XY:
49
AN XY:
319730
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:
0.000227
Gnomad4 OTH exome
AF:
0.000331
GnomAD4 genome
AF:
0.0000978
AC:
11
AN:
112508
Hom.:
0
Cov.:
23
AF XY:
0.000144
AC XY:
5
AN XY:
34640
show subpopulations
Gnomad4 AFR
AF:
0.0000323
Gnomad4 AMR
AF:
0.0000940
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000169
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000142
Hom.:
1
Bravo
AF:
0.000125
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000301
AC:
2
ExAC
AF:
0.0000851
AC:
10

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 08, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.22G>C (p.A8P) alteration is located in exon 1 (coding exon 1) of the TSR2 gene. This alteration results from a G to C substitution at nucleotide position 22, causing the alanine (A) at amino acid position 8 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

not provided Uncertain:1
Nov 10, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 8 of the TSR2 protein (p.Ala8Pro). This variant is present in population databases (rs377577583, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with TSR2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2262503). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.47
T
BayesDel_noAF
Benign
-0.73
CADD
Benign
7.0
DANN
Benign
0.84
DEOGEN2
Benign
0.024
T
FATHMM_MKL
Benign
0.00038
N
LIST_S2
Benign
0.54
T
M_CAP
Benign
0.047
D
MetaRNN
Benign
0.044
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.34
N
PrimateAI
Uncertain
0.57
T
PROVEAN
Benign
-0.070
N
REVEL
Benign
0.050
Sift
Benign
0.27
T
Sift4G
Benign
0.23
T
Polyphen
0.23
B
Vest4
0.14
MVP
0.25
MPC
0.70
ClinPred
0.041
T
GERP RS
-0.54
Varity_R
0.084
gMVP
0.71

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: rs377577583; hg19: chrX-54466876; API