Genetic Variant MTFP1:c.196-93G>A (chr22-30427078-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016498.5(MTFP1):c.196-93G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 1,450,784 control chromosomes in the GnomAD database, including 51,355 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 0.28 ( 6195 hom., cov: 32)

Exomes 𝑓: 0.26 ( 45160 hom. )

Consequence

MTFP1
NM_016498.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.143

Publications

8 publications found

Variant links:

Genes affected

MTFP1 (HGNC:26945): (mitochondrial fission process 1) MTP18 is a mitochondrial protein and downstream target of the phosphatidylinositol 3-kinase (see PIK3CA, MIM 171834) signaling pathway that plays a role in cell viability and mitochondrial dynamics (Tondera et al., 2004 [PubMed 15155745]).[supplied by OMIM, Mar 2008]

MTFP1 links:

ENSG00000249590 (HGNC:):

ENSG00000249590 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016498.5. 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
	MTFP1	NM_016498.5	MANE Select	c.196-93G>A		intron	N/A	NP_057582.2	Q9UDX5-1
	MTFP1	NM_001003704.3		c.195+234G>A		intron	N/A	NP_001003704.1	Q9UDX5-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MTFP1	ENST00000266263.10	TSL:1 MANE Select	c.196-93G>A	intron	N/A	ENSP00000266263.5	Q9UDX5-1
ENSG00000249590	ENST00000439838.5	TSL:2	c.712-93G>A	intron	N/A	ENSP00000415178.1	H7C417
MTFP1	ENST00000862422.1		c.196-24G>A	intron	N/A	ENSP00000532481.1

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42926

AN:

151956

Hom.:

6192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.364

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.266

GnomAD2 exomes

AF:

0.277

AC:

67687

AN:

244282

AF XY:

0.277

show subpopulations

Gnomad AFR exome

AF:

0.317

Gnomad AMR exome

AF:

0.317

Gnomad ASJ exome

AF:

0.209

Gnomad EAS exome

AF:

0.278

Gnomad FIN exome

AF:

0.286

Gnomad NFE exome

AF:

0.251

Gnomad OTH exome

AF:

0.271

GnomAD4 exome

AF:

0.260

AC:

338072

AN:

1298710

Hom.:

45160

Cov.:

AF XY:

0.262

AC XY:

171668

AN XY:

654392

show subpopulations

African (AFR)

AF:

0.314

AC:

9468

AN:

30170

American (AMR)

AF:

0.317

AC:

14039

AN:

44270

Ashkenazi Jewish (ASJ)

AF:

0.207

AC:

5203

AN:

25098

East Asian (EAS)

AF:

0.270

AC:

10496

AN:

38834

South Asian (SAS)

AF:

0.322

AC:

26474

AN:

82148

European-Finnish (FIN)

AF:

0.291

AC:

15188

AN:

52174

Middle Eastern (MID)

AF:

0.327

AC:

1608

AN:

4916

European-Non Finnish (NFE)

AF:

0.249

AC:

240966

AN:

966210

Other (OTH)

AF:

0.267

AC:

14630

AN:

54890

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

14055

28110

42165

56220

70275

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7790

15580

23370

31160

38950

<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:

0.282

AC:

42956

AN:

152074

Hom.:

6195

Cov.:

AF XY:

0.285

AC XY:

21154

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.318

AC:

13203

AN:

41478

American (AMR)

AF:

0.290

AC:

4435

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

727

AN:

3468

East Asian (EAS)

AF:

0.266

AC:

1380

AN:

5182

South Asian (SAS)

AF:

0.319

AC:

1535

AN:

4818

European-Finnish (FIN)

AF:

0.287

AC:

3042

AN:

10588

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.260

AC:

17645

AN:

67950

Other (OTH)

AF:

0.273

AC:

575

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1598

3196

4794

6392

7990

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<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:

0.263

Hom.:

6988

Bravo

AF:

0.282

Asia WGS

AF:

0.327

AC:

1135

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.2

(source)

DANN

Benign

0.85

PhyloP100

-0.14

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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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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