rs549699802

Variant names:

• chr9-129040620-C-G
• rs549699802
• NM_001329990.2:c.26C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-129040620-C-G
• chr9-129040620-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001329990.2(MIGA2):​c.26C>G​(p.Thr9Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T9M) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MIGA2 NM_001329990.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.56
• Publications: 3 publications found

Genes affected

MIGA2 (HGNC:23621): (mitoguardin 2) Enables protein heterodimerization activity and protein homodimerization activity. Involved in mitochondrial fusion. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15542853).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329990.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIGA2	NM_001329990.2	MANE Select	c.26C>G	p.Thr9Arg	missense	Exon 2 of 16	NP_001316919.1	Q7L4E1-1
	MIGA2	NM_032809.4		c.218C>G	p.Thr73Arg	missense	Exon 2 of 16	NP_116198.3
	MIGA2	NR_138421.2		n.225C>G		non_coding_transcript_exon	Exon 2 of 17

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIGA2	ENST00000684074.1	MANE Select	c.26C>G	p.Thr9Arg	missense	Exon 2 of 16	ENSP00000506871.1	Q7L4E1-1
	MIGA2	ENST00000358369.8	TSL:1	c.26C>G	p.Thr9Arg	missense	Exon 2 of 16	ENSP00000351138.4	Q7L4E1-1
	MIGA2	ENST00000942817.1		c.26C>G	p.Thr9Arg	missense	Exon 2 of 16	ENSP00000612876.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	21
DANN	Benign	0.91
DEOGEN2	Benign	0.0062	T
Eigen	Benign	-0.46
Eigen_PC	Benign	-0.29
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Uncertain	0.86	D
M_CAP	Benign	0.027	D
MetaRNN	Benign	0.16	T
MetaSVM	Benign	-1.0	T
PhyloP100		5.6
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-0.41	N
REVEL	Benign	0.13
Sift	Uncertain	0.014	D
Sift4G	Benign	0.71	T
Polyphen		0.065	B
Vest4		0.41
MutPred		0.36		Gain of MoRF binding (P = 0.0026)
MVP		0.46
MPC		0.39
ClinPred		0.51	D
GERP RS		4.3
Varity_R		0.16
gMVP		0.60
Mutation Taster		=84/16	polymorphism

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: rs549699802; hg19: chr9-131802899;