7-6009432-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Moderate BP6_Moderate

The NM_006303.4(AIMP2):c.69C>T(p.Cys23=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0004 in 1,611,244 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00032 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00041 (3 hom.)
• Consequence: AIMP2 NM_006303.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 6.20

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BP6: Variant 7-6009432-C-T is Benign according to our data. Variant chr7-6009432-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1571764.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AIMP2	NM_006303.4	c.69C>T	p.Cys23=	synonymous_variant	1/4	ENST00000223029.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AIMP2	ENST00000223029.8	c.69C>T	p.Cys23=	synonymous_variant	1/4	1	NM_006303.4	P1
AIMP2	ENST00000395236.2	c.69C>T	p.Cys23=	synonymous_variant	1/3	2
AIMP2	ENST00000400479.6	c.-251+54C>T		intron_variant		5
AIMP2	ENST00000415999.1	c.69C>T	p.Cys23=	synonymous_variant, NMD_transcript_variant	1/3	3

Frequencies

GnomAD3 genomes AF: 0.000322 AC: 49 AN: 152168 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000413

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000588

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.000217 AC: 54 AN: 248978 Hom.: 1 AF XY: 0.000215 AC XY: 29 AN XY: 135166

Gnomad AFR exome AF: 0.000125

Gnomad AMR exome AF: 0.0000580

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000229

Gnomad FIN exome AF: 0.000139

Gnomad NFE exome AF: 0.000357

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000409 AC: 596 AN: 1458958 Hom.: 3 Cov.: 33 AF XY: 0.000413 AC XY: 300 AN XY: 725782

Gnomad4 AFR exome AF: 0.0000599

Gnomad4 AMR exome AF: 0.0000672

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000395

Gnomad4 FIN exome AF: 0.0000759

Gnomad4 NFE exome AF: 0.000477

Gnomad4 OTH exome AF: 0.000382

GnomAD4 genome AF: 0.000322 AC: 49 AN: 152286 Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26 AN XY: 74468

Gnomad4 AFR AF: 0.0000962

Gnomad4 AMR AF: 0.0000653

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.000588

Gnomad4 OTH AF: 0.000474

Alfa AF: 0.000442 Hom.: 1

Bravo AF: 0.000257

EpiCase AF: 0.000927

EpiControl AF: 0.000474

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Mar 21, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
Cadd	Benign	16
Dann	Benign	0.96
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs201425558; hg19: chr7-6049063; COSMIC: COSV56151146; COSMIC: COSV56151146;