Variant 22-30427161-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000266263.10(MTFP1):c.196-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00484 in 1,613,392 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0043 ( 10 hom., cov: 33)

Exomes 𝑓: 0.0049 ( 33 hom. )

Consequence

MTFP1
ENST00000266263.10 intron

Scores

Splicing: ADA: 0.00004452

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.261

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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 22-30427161-C-T is Benign according to our data. Variant chr22-30427161-C-T is described in ClinVar as [Benign]. Clinvar id is 719271.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0049 (7154/1461050) while in subpopulation MID AF= 0.0179 (103/5764). AF 95% confidence interval is 0.0151. There are 33 homozygotes in gnomad4_exome. There are 3525 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTFP1	NM_016498.5 linkuse as main transcript	c.196-10C>T		intron_variant		ENST00000266263.10	NP_057582.2	Q9UDX5-1A0A024R1E4
MTFP1	NM_001003704.3 linkuse as main transcript	c.195+317C>T		intron_variant			NP_001003704.1	Q9UDX5-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTFP1	ENST00000266263.10 linkuse as main transcript	c.196-10C>T		intron_variant		1	NM_016498.5	ENSP00000266263.5		Q9UDX5-1
ENSG00000249590	ENST00000439838.5 linkuse as main transcript	c.712-10C>T		intron_variant		2		ENSP00000415178.1		H7C417

Frequencies

GnomAD3 genomes

AF:

0.00426

AC:

648

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00128

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.00641

Gnomad ASJ

AF:

0.0141

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.000847

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00588

Gnomad OTH

AF:

0.00908

GnomAD3 exomes

AF:

0.00434

AC:

1089

AN:

251140

Hom.:

AF XY:

0.00430

AC XY:

584

AN XY:

135798

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00309

Gnomad ASJ exome

AF:

0.0186

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00131

Gnomad FIN exome

AF:

0.000835

Gnomad NFE exome

AF:

0.00593

Gnomad OTH exome

AF:

0.00734

GnomAD4 exome

AF:

0.00490

AC:

7154

AN:

1461050

Hom.:

Cov.:

AF XY:

0.00485

AC XY:

3525

AN XY:

726872

show subpopulations

Gnomad4 AFR exome

AF:

0.000956

Gnomad4 AMR exome

AF:

0.00333

Gnomad4 ASJ exome

AF:

0.0186

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00119

Gnomad4 FIN exome

AF:

0.000957

Gnomad4 NFE exome

AF:

0.00525

Gnomad4 OTH exome

AF:

0.00658

GnomAD4 genome

AF:

0.00425

AC:

648

AN:

152342

Hom.:

Cov.:

AF XY:

0.00408

AC XY:

304

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00128

Gnomad4 AMR

AF:

0.00640

Gnomad4 ASJ

AF:

0.0141

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.000847

Gnomad4 NFE

AF:

0.00588

Gnomad4 OTH

AF:

0.00899

Alfa

AF:

0.00583

Hom.:

Bravo

AF:

0.00471

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 28, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.9

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000045

dbscSNV1_RF

Benign

0.0060

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over