chr10-121743672-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001001976.3(ATE1):​c.*8A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,597,688 control chromosomes in the GnomAD database, including 24,133 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.23 ( 5647 hom., cov: 32)
Exomes 𝑓: 0.14 ( 18486 hom. )

Consequence

ATE1
NM_001001976.3 3_prime_UTR

Scores

2

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.93
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 10-121743672-T-C is Benign according to our data. Variant chr10-121743672-T-C is described in ClinVar as [Benign]. Clinvar id is 3059476.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATE1NM_001001976.3 linkuse as main transcriptc.*8A>G 3_prime_UTR_variant 12/12 ENST00000224652.12 NP_001001976.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATE1ENST00000224652.12 linkuse as main transcriptc.*8A>G 3_prime_UTR_variant 12/121 NM_001001976.3 ENSP00000224652 A1O95260-1

Frequencies

GnomAD3 genomes
AF:
0.234
AC:
35538
AN:
151886
Hom.:
5631
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.438
Gnomad AMI
AF:
0.216
Gnomad AMR
AF:
0.302
Gnomad ASJ
AF:
0.143
Gnomad EAS
AF:
0.0727
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.194
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.120
Gnomad OTH
AF:
0.197
GnomAD3 exomes
AF:
0.192
AC:
45791
AN:
238390
Hom.:
6063
AF XY:
0.182
AC XY:
23499
AN XY:
128860
show subpopulations
Gnomad AFR exome
AF:
0.446
Gnomad AMR exome
AF:
0.367
Gnomad ASJ exome
AF:
0.139
Gnomad EAS exome
AF:
0.0658
Gnomad SAS exome
AF:
0.224
Gnomad FIN exome
AF:
0.189
Gnomad NFE exome
AF:
0.123
Gnomad OTH exome
AF:
0.162
GnomAD4 exome
AF:
0.141
AC:
203411
AN:
1445684
Hom.:
18486
Cov.:
32
AF XY:
0.141
AC XY:
101414
AN XY:
718202
show subpopulations
Gnomad4 AFR exome
AF:
0.457
Gnomad4 AMR exome
AF:
0.359
Gnomad4 ASJ exome
AF:
0.137
Gnomad4 EAS exome
AF:
0.0705
Gnomad4 SAS exome
AF:
0.223
Gnomad4 FIN exome
AF:
0.186
Gnomad4 NFE exome
AF:
0.116
Gnomad4 OTH exome
AF:
0.159
GnomAD4 genome
AF:
0.234
AC:
35608
AN:
152004
Hom.:
5647
Cov.:
32
AF XY:
0.237
AC XY:
17592
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.438
Gnomad4 AMR
AF:
0.302
Gnomad4 ASJ
AF:
0.143
Gnomad4 EAS
AF:
0.0725
Gnomad4 SAS
AF:
0.231
Gnomad4 FIN
AF:
0.194
Gnomad4 NFE
AF:
0.120
Gnomad4 OTH
AF:
0.207
Alfa
AF:
0.137
Hom.:
755
Bravo
AF:
0.251
Asia WGS
AF:
0.206
AC:
715
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

ATE1-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesOct 28, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.95
DANN
Benign
0.76

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: rs10886973; hg19: chr10-123503187; API