chr10-121841098-C-T

Variant summary

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

The NM_001001976.3(ATE1):​c.1141G>A​(p.Val381Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000685 in 1,562,440 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000069 ( 1 hom. )

Consequence

ATE1
NM_001001976.3 missense

Scores

8
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.30
Variant links:
Genes affected
ATE1 (HGNC:782): (arginyltransferase 1) This gene encodes an arginyltransferase, an enzyme that is involved in posttranslational conjugation of arginine to N-terminal aspartate or glutamate residues. Conjugation of arginine to the N-terminal aspartate or glutamate targets proteins for ubiquitin-dependent degradation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

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=0.090883136).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATE1NM_001001976.3 linkuse as main transcriptc.1141G>A p.Val381Ile missense_variant 9/12 ENST00000224652.12 NP_001001976.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATE1ENST00000224652.12 linkuse as main transcriptc.1141G>A p.Val381Ile missense_variant 9/121 NM_001001976.3 ENSP00000224652 A1O95260-1

Frequencies

GnomAD3 genomes
AF:
0.0000658
AC:
10
AN:
151966
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000656
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00125
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000156
AC:
37
AN:
237860
Hom.:
0
AF XY:
0.000194
AC XY:
25
AN XY:
129048
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000590
Gnomad SAS exome
AF:
0.00103
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000555
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000688
AC:
97
AN:
1410356
Hom.:
1
Cov.:
31
AF XY:
0.0000928
AC XY:
65
AN XY:
700702
show subpopulations
Gnomad4 AFR exome
AF:
0.000124
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000261
Gnomad4 SAS exome
AF:
0.000910
Gnomad4 FIN exome
AF:
0.0000196
Gnomad4 NFE exome
AF:
0.0000148
Gnomad4 OTH exome
AF:
0.0000866
GnomAD4 genome
AF:
0.0000658
AC:
10
AN:
152084
Hom.:
0
Cov.:
32
AF XY:
0.0000673
AC XY:
5
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.0000655
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00125
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000330
Hom.:
0
Bravo
AF:
0.0000340
ExAC
AF:
0.000165
AC:
20

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 GeneticsJul 05, 2023The c.1141G>A (p.V381I) alteration is located in exon 9 (coding exon 9) of the ATE1 gene. This alteration results from a G to A substitution at nucleotide position 1141, causing the valine (V) at amino acid position 381 to be replaced by an isoleucine (I). 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
0.091
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.37
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.22
T;T;T;T;.
Eigen
Uncertain
0.58
Eigen_PC
Uncertain
0.60
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Uncertain
0.91
D;D;D;D;D
M_CAP
Benign
0.0041
T
MetaRNN
Benign
0.091
T;T;T;T;T
MetaSVM
Benign
-0.38
T
MutationAssessor
Benign
2.0
M;.;.;.;M
MutationTaster
Benign
1.0
D;D;D;D;D;D
PrimateAI
Uncertain
0.60
T
PROVEAN
Benign
-0.90
N;N;N;N;N
REVEL
Benign
0.16
Sift
Uncertain
0.013
D;D;D;D;D
Sift4G
Uncertain
0.016
D;D;D;D;D
Polyphen
0.98
D;D;.;D;D
Vest4
0.23
MutPred
0.69
Loss of phosphorylation at Y382 (P = 0.1497);.;.;.;Loss of phosphorylation at Y382 (P = 0.1497);
MVP
0.15
MPC
0.13
ClinPred
0.15
T
GERP RS
5.6
Varity_R
0.13
gMVP
0.36

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: rs538914300; hg19: chr10-123600613; COSMIC: COSV56443508; COSMIC: COSV56443508; API