rs17508321

Variant names:

• chr9-129049897-C-T
• rs17508321
• NM_001329990.2:c.609C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-129049897-C-T
• chr9-129049897-C-A
• chr9-129049897-C-G

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_001329990.2(MIGA2):​c.609C>T​(p.Ser203Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00425 in 1,613,810 control chromosomes in the GnomAD database, including 142 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.017 (71 hom., cov: 32)
  • Exomes 𝑓: 0.0030 (71 hom.)
• Consequence: MIGA2 NM_001329990.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.23
• Publications: 1 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: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP6: Variant 9-129049897-C-T is Benign according to our data. Variant chr9-129049897-C-T is described in ClinVar as Benign. ClinVar VariationId is 774439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-1.23 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

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.609C>T	p.Ser203Ser	synonymous	Exon 6 of 16	NP_001316919.1	Q7L4E1-1
	MIGA2	NM_032809.4		c.801C>T	p.Ser267Ser	synonymous	Exon 6 of 16	NP_116198.3
	MIGA2	NR_138421.2		n.808C>T		non_coding_transcript_exon	Exon 6 of 17

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIGA2	ENST00000684074.1	MANE Select	c.609C>T	p.Ser203Ser	synonymous	Exon 6 of 16	ENSP00000506871.1	Q7L4E1-1
	MIGA2	ENST00000358369.8	TSL:1	c.609C>T	p.Ser203Ser	synonymous	Exon 6 of 16	ENSP00000351138.4	Q7L4E1-1
	MIGA2	ENST00000942817.1		c.609C>T	p.Ser203Ser	synonymous	Exon 6 of 16	ENSP00000612876.1

Frequencies

GnomAD3 genomes AF: 0.0167 AC: 2535 AN: 152166 Hom.: 71 Cov.: 32

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0116

Gnomad ASJ AF: 0.00979

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00146

Gnomad OTH AF: 0.0191

GnomAD2 exomes AF: 0.00592 AC: 1485 AN: 250854 AF XY: 0.00470

Gnomad AFR exome AF: 0.0568

Gnomad AMR exome AF: 0.00672

Gnomad ASJ exome AF: 0.0115

Gnomad EAS exome AF: 0.0000545

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00144

Gnomad OTH exome AF: 0.00605

GnomAD4 exome AF: 0.00295 AC: 4312 AN: 1461526 Hom.: 71 Cov.: 32 AF XY: 0.00284 AC XY: 2066 AN XY: 727080

African (AFR) AF: 0.0586 AC: 1960 AN: 33474

American (AMR) AF: 0.00694 AC: 310 AN: 44694

Ashkenazi Jewish (ASJ) AF: 0.0122 AC: 319 AN: 26132

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.000696 AC: 60 AN: 86254

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53136

Middle Eastern (MID) AF: 0.00746 AC: 43 AN: 5766

European-Non Finnish (NFE) AF: 0.00108 AC: 1198 AN: 1111988

Other (OTH) AF: 0.00699 AC: 422 AN: 60382

GnomAD4 genome AF: 0.0168 AC: 2553 AN: 152284 Hom.: 71 Cov.: 32 AF XY: 0.0164 AC XY: 1225 AN XY: 74470

African (AFR) AF: 0.0527 AC: 2191 AN: 41548

American (AMR) AF: 0.0116 AC: 177 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00979 AC: 34 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00146 AC: 99 AN: 68022

Other (OTH) AF: 0.0189 AC: 40 AN: 2112

Alfa AF: 0.00881 Hom.: 17

Bravo AF: 0.0192

Asia WGS AF: 0.00375 AC: 13 AN: 3478

EpiCase AF: 0.00180

EpiControl AF: 0.00148

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs17508321; hg19: chr9-131812176; COSMIC: COSV52977948; COSMIC: COSV52977948;