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GeneBe

rs4560

chr7-6023652-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_006303.4(AIMP2):c.924C>T(p.Asn308=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 1,613,692 control chromosomes in the GnomAD database, including 132,474 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.35 ( 10008 hom., cov: 32)
Exomes 𝑓: 0.41 ( 122466 hom. )

Consequence

AIMP2
NM_006303.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.36
Variant links:
Genes affected
AIMP2 (HGNC:20609): (aminoacyl tRNA synthetase complex interacting multifunctional protein 2) The protein encoded by this gene is part of the aminoacyl-tRNA synthetase complex, which contains nine different aminoacyl-tRNA synthetases and three non-enzymatic factors. The encoded protein is one of the non-enzymatic factors and is required for assembly and stability of the complex. [provided by RefSeq, May 2016]
EIF2AK1 (HGNC:24921): (eukaryotic translation initiation factor 2 alpha kinase 1) The protein encoded by this gene acts at the level of translation initiation to downregulate protein synthesis in response to stress. The encoded protein is a kinase that can be inactivated by hemin. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-6023652-C-T is Benign according to our data. Variant chr7-6023652-C-T is described in ClinVar as [Benign]. Clinvar id is 1166059.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=2.36 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AIMP2NM_006303.4 linkuse as main transcriptc.924C>T p.Asn308= synonymous_variant 4/4 ENST00000223029.8
EIF2AK1NM_014413.4 linkuse as main transcriptc.*1021G>A 3_prime_UTR_variant 15/15 ENST00000199389.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AIMP2ENST00000223029.8 linkuse as main transcriptc.924C>T p.Asn308= synonymous_variant 4/41 NM_006303.4 P1Q13155-1
EIF2AK1ENST00000199389.11 linkuse as main transcriptc.*1021G>A 3_prime_UTR_variant 15/151 NM_014413.4 P1Q9BQI3-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.346
AC:
52495
AN:
151802
Hom.:
10003
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.190
Gnomad AMI
AF:
0.390
Gnomad AMR
AF:
0.363
Gnomad ASJ
AF:
0.438
Gnomad EAS
AF:
0.383
Gnomad SAS
AF:
0.343
Gnomad FIN
AF:
0.348
Gnomad MID
AF:
0.462
Gnomad NFE
AF:
0.427
Gnomad OTH
AF:
0.368
GnomAD3 exomes
AF:
0.376
AC:
93532
AN:
248868
Hom.:
18184
AF XY:
0.383
AC XY:
51628
AN XY:
134734
show subpopulations
Gnomad AFR exome
AF:
0.185
Gnomad AMR exome
AF:
0.325
Gnomad ASJ exome
AF:
0.440
Gnomad EAS exome
AF:
0.381
Gnomad SAS exome
AF:
0.347
Gnomad FIN exome
AF:
0.343
Gnomad NFE exome
AF:
0.426
Gnomad OTH exome
AF:
0.392
GnomAD4 exome
AF:
0.406
AC:
593549
AN:
1461772
Hom.:
122466
Cov.:
57
AF XY:
0.407
AC XY:
295764
AN XY:
727180
show subpopulations
Gnomad4 AFR exome
AF:
0.177
Gnomad4 AMR exome
AF:
0.329
Gnomad4 ASJ exome
AF:
0.442
Gnomad4 EAS exome
AF:
0.384
Gnomad4 SAS exome
AF:
0.352
Gnomad4 FIN exome
AF:
0.344
Gnomad4 NFE exome
AF:
0.423
Gnomad4 OTH exome
AF:
0.398
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.346
AC:
52515
AN:
151920
Hom.:
10008
Cov.:
32
AF XY:
0.342
AC XY:
25387
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.190
Gnomad4 AMR
AF:
0.363
Gnomad4 ASJ
AF:
0.438
Gnomad4 EAS
AF:
0.384
Gnomad4 SAS
AF:
0.344
Gnomad4 FIN
AF:
0.348
Gnomad4 NFE
AF:
0.427
Gnomad4 OTH
AF:
0.365
Alfa
AF:
0.414
Hom.:
27216
Bravo
AF:
0.340
Asia WGS
AF:
0.315
AC:
1099
AN:
3478
EpiCase
AF:
0.438
EpiControl
AF:
0.440

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 30, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
Cadd
Benign
12
Dann
Benign
0.90

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.10
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: rs4560; hg19: chr7-6063283; COSMIC: COSV52236293; COSMIC: COSV52236293; API