Genetic Variant MTFMT:c.*99dupT (chr15-65002962-C-CA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_139242.4(MTFMT):c.*99dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.44 ( 7522 hom., cov: 0)

Exomes 𝑓: 0.27 ( 134 hom. )

Consequence

MTFMT
NM_139242.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.893

Publications

0 publications found

Variant links:

Genes affected

MTFMT (HGNC:29666): (mitochondrial methionyl-tRNA formyltransferase) The protein encoded by this nuclear gene localizes to the mitochondrion, where it catalyzes the formylation of methionyl-tRNA. [provided by RefSeq, Jun 2011]

MTFMT Gene-Disease associations (from GenCC):

combined oxidative phosphorylation defect type 15
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
Leigh syndrome
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
Leigh syndrome with leukodystrophy
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

MTFMT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 15-65002962-C-CA is Benign according to our data. Variant chr15-65002962-C-CA is described in ClinVar as Benign. ClinVar VariationId is 1237194.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139242.4. 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
	MTFMT	NM_139242.4	MANE Select	c.*99dupT		3_prime_UTR	Exon 9 of 9	NP_640335.2	Q96DP5-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MTFMT	ENST00000220058.9	TSL:1 MANE Select	c.*99dupT	3_prime_UTR	Exon 9 of 9	ENSP00000220058.4	Q96DP5-1
MTFMT	ENST00000901062.1		c.*99dupT	3_prime_UTR	Exon 10 of 10	ENSP00000571121.1
MTFMT	ENST00000901059.1		c.*99dupT	3_prime_UTR	Exon 9 of 9	ENSP00000571118.1

Frequencies

GnomAD3 genomes

AF:

0.442

AC:

26939

AN:

60890

Hom.:

7523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.549

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.594

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.376

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.425

GnomAD4 exome

AF:

0.273

AC:

71718

AN:

263134

Hom.:

134

Cov.:

AF XY:

0.272

AC XY:

36300

AN XY:

133580

show subpopulations

African (AFR)

AF:

0.202

AC:

1329

AN:

6590

American (AMR)

AF:

0.207

AC:

1206

AN:

5814

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

1572

AN:

5554

East Asian (EAS)

AF:

0.188

AC:

2867

AN:

15226

South Asian (SAS)

AF:

0.210

AC:

2120

AN:

10076

European-Finnish (FIN)

AF:

0.262

AC:

3323

AN:

12692

Middle Eastern (MID)

AF:

0.288

AC:

299

AN:

1038

European-Non Finnish (NFE)

AF:

0.288

AC:

55513

AN:

193080

Other (OTH)

AF:

0.267

AC:

3489

AN:

13064

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.415

Heterozygous variant carriers

2725

5450

8175

10900

13625

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1666

3332

4998

6664

8330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.442

AC:

26923

AN:

60872

Hom.:

7522

Cov.:

AF XY:

0.426

AC XY:

11727

AN XY:

27518

show subpopulations

African (AFR)

AF:

0.193

AC:

2768

AN:

14340

American (AMR)

AF:

0.325

AC:

1634

AN:

5022

Ashkenazi Jewish (ASJ)

AF:

0.594

AC:

1078

AN:

1814

East Asian (EAS)

AF:

0.160

AC:

292

AN:

1828

South Asian (SAS)

AF:

0.491

AC:

844

AN:

1720

European-Finnish (FIN)

AF:

0.376

AC:

565

AN:

1504

Middle Eastern (MID)

AF:

0.490

AC:

AN:

European-Non Finnish (NFE)

AF:

0.574

AC:

19077

AN:

33248

Other (OTH)

AF:

0.424

AC:

325

AN:

766

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.549

Heterozygous variant carriers

527

1054

1581

2108

2635

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.89

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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15-65002962-CAAAAAAAAAAA-CAAAAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over