NM_006303.4:c.343-961G>C

Variant names:

• chr7-6016853-G-C
• rs3779109
• NM_006303.4:c.343-961G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006303.4(AIMP2):​c.343-961G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 153,332 control chromosomes in the GnomAD database, including 3,829 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 0.21 (3807 hom., cov: 32)
  • Exomes 𝑓: 0.19 (22 hom.)
• Consequence: AIMP2 NM_006303.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 8 publications found

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]

SNORA80D (HGNC:50435): (small nucleolar RNA, H/ACA box 80D)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006303.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AIMP2	NM_006303.4	MANE Select	c.343-961G>C		intron	N/A	NP_006294.2
	AIMP2	NM_001362785.2		c.256-961G>C		intron	N/A	NP_001349714.1
	AIMP2	NM_001326606.2		c.223-961G>C		intron	N/A	NP_001313535.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AIMP2	ENST00000223029.8	TSL:1 MANE Select	c.343-961G>C		intron	N/A	ENSP00000223029.3
	AIMP2	ENST00000395236.2	TSL:2	c.136-961G>C		intron	N/A	ENSP00000378658.2
	AIMP2	ENST00000400479.6	TSL:5	c.109-961G>C		intron	N/A	ENSP00000383327.2

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32562 AN: 151948 Hom.: 3805 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.194 AC: 245 AN: 1264 Hom.: 22 Cov.: 0 AF XY: 0.204 AC XY: 131 AN XY: 642

African (AFR) AF: 0.289 AC: 11 AN: 38

American (AMR) AF: 0.167 AC: 1 AN: 6

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.538 AC: 14 AN: 26

South Asian (SAS) AF: 0.156 AC: 5 AN: 32

European-Finnish (FIN) AF: 0.292 AC: 21 AN: 72

Middle Eastern (MID) AF: 0.176 AC: 153 AN: 870

European-Non Finnish (NFE) AF: 0.160 AC: 15 AN: 94

Other (OTH) AF: 0.198 AC: 25 AN: 126

GnomAD4 genome AF: 0.214 AC: 32574 AN: 152068 Hom.: 3807 Cov.: 32 AF XY: 0.220 AC XY: 16358 AN XY: 74332

African (AFR) AF: 0.229 AC: 9482 AN: 41462

American (AMR) AF: 0.168 AC: 2573 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2106 AN: 5162

South Asian (SAS) AF: 0.316 AC: 1521 AN: 4816

European-Finnish (FIN) AF: 0.268 AC: 2829 AN: 10566

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12409 AN: 67992

Other (OTH) AF: 0.210 AC: 445 AN: 2116

Alfa AF: 0.107 Hom.: 169

Bravo AF: 0.207

Asia WGS AF: 0.360 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.77
PhyloP100		-0.093
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3779109; hg19: chr7-6056484; COSMIC: COSV56152065; COSMIC: COSV56152065;