dbSNP rs2072159: 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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTFP1	NM_016498.5 link	c.196-93G>A		intron_variant	Intron 2 of 3	ENST00000266263.10	NP_057582.2	Q9UDX5-1A0A024R1E4
MTFP1	NM_001003704.3 link	c.195+234G>A		intron_variant	Intron 2 of 2		NP_001003704.1	Q9UDX5-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTFP1	ENST00000266263.10 link	c.196-93G>A		intron_variant	Intron 2 of 3	1	NM_016498.5	ENSP00000266263.5		Q9UDX5-1
ENSG00000249590	ENST00000439838.5 link	c.712-93G>A		intron_variant	Intron 7 of 8	2		ENSP00000415178.1		H7C417

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over