rs1860460

Positions:

• chr7-6013655-G-A
• chr7-6013655-G-C
• chr7-6013655-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006303.4(AIMP2):​c.136-1491G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,000 control chromosomes in the GnomAD database, including 33,083 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (33083 hom., cov: 32)
• Consequence: AIMP2 NM_006303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AIMP2	NM_006303.4	c.136-1491G>A		intron_variant		ENST00000223029.8	NP_006294.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AIMP2	ENST00000223029.8	c.136-1491G>A		intron_variant		1	NM_006303.4	ENSP00000223029	P1
AIMP2	ENST00000395236.2	c.135+4157G>A		intron_variant		2		ENSP00000378658
AIMP2	ENST00000400479.6	c.-250-1247G>A		intron_variant		5		ENSP00000383327
AIMP2	ENST00000415999.1	c.*450+515G>A		intron_variant, NMD_transcript_variant		3		ENSP00000392519

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99068 AN: 151882 Hom.: 33077 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.677

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.652 AC: 99109 AN: 152000 Hom.: 33083 Cov.: 32 AF XY: 0.654 AC XY: 48587 AN XY: 74288

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.678

Alfa AF: 0.679 Hom.: 28948

Bravo AF: 0.636

Asia WGS AF: 0.772 AC: 2685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs1860460; hg19: chr7-6053286;