Variant rs4560 details in Genebe, Genetics Data Aggregator

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

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]

AIMP2 links:

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]

EIF2AK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

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

Synonymous conserved (PhyloP=2.36 with no splicing effect.

BA1

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	Protein	UniProt
AIMP2	NM_006303.4 linkuse as main transcript	c.924C>T	p.Asn308=	synonymous_variant	4/4	ENST00000223029.8	NP_006294.2
EIF2AK1	NM_014413.4 linkuse as main transcript	c.*1021G>A		3_prime_UTR_variant	15/15	ENST00000199389.11	NP_055228.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AIMP2	ENST00000223029.8 linkuse as main transcript	c.924C>T	p.Asn308=	synonymous_variant	4/4	1	NM_006303.4	ENSP00000223029	P1	Q13155-1
EIF2AK1	ENST00000199389.11 linkuse as main transcript	c.*1021G>A		3_prime_UTR_variant	15/15	1	NM_014413.4	ENSP00000199389	P1	Q9BQI3-1

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52495

AN:

151802

Hom.:

10003

Cov.:

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.:

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

AF:

0.346

AC:

52515

AN:

151920

Hom.:

10008

Cov.:

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over