Genetic Variant MTFMT:c.*94_*99delTTTTTT (chr15-65002962-CAAAAAA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_139242.4(MTFMT):c.*94_*99delTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000313 in 325,678 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00030 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00032 ( 0 hom. )

Consequence

MTFMT
NM_139242.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.840

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: Uncertain_significance. The variant received 0 ACMG points.

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.94_99delTTTTTT		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.94_99delTTTTTT	3_prime_UTR	Exon 9 of 9	ENSP00000220058.4	Q96DP5-1
MTFMT	ENST00000901062.1		c.94_99delTTTTTT	3_prime_UTR	Exon 10 of 10	ENSP00000571121.1
MTFMT	ENST00000901059.1		c.94_99delTTTTTT	3_prime_UTR	Exon 9 of 9	ENSP00000571118.1

Frequencies

GnomAD3 genomes

AF:

0.000296

AC:

AN:

60764

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000348

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00139

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000151

Gnomad OTH

AF:

0.00132

GnomAD4 exome

AF:

0.000317

AC:

AN:

264932

Hom.:

AF XY:

0.000335

AC XY:

AN XY:

134488

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000301

AC:

AN:

6634

American (AMR)

AF:

0.000851

AC:

AN:

5878

Ashkenazi Jewish (ASJ)

AF:

0.000356

AC:

AN:

5618

East Asian (EAS)

AF:

0.000260

AC:

AN:

15410

South Asian (SAS)

AF:

0.000395

AC:

AN:

10124

European-Finnish (FIN)

AF:

0.0000783

AC:

AN:

12768

Middle Eastern (MID)

AF:

0.000956

AC:

AN:

1046

European-Non Finnish (NFE)

AF:

0.000304

AC:

AN:

194268

Other (OTH)

AF:

0.000455

AC:

AN:

13186

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000000117876), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.393

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.000296

AC:

AN:

60746

Hom.:

Cov.:

AF XY:

0.000182

AC XY:

AN XY:

27454

show subpopulations

African (AFR)

AF:

0.000348

AC:

AN:

14386

American (AMR)

AF:

0.00139

AC:

AN:

5018

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1806

East Asian (EAS)

AF:

0.00

AC:

AN:

1830

South Asian (SAS)

AF:

0.00

AC:

AN:

1718

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1498

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000151

AC:

AN:

33104

Other (OTH)

AF:

0.00131

AC:

AN:

762

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.583

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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15-65002962-CAAAAAAAAAAA-CAAAAA

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