Variant chr2-227329923-T-TA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001277062.2(MFF):c.-40-692dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.66 ( 32473 hom., cov: 0)

Exomes 𝑓: 0.48 ( 7280 hom. )

Consequence

MFF
NM_001277062.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0110

Variant links:

Genes affected

MFF (HGNC:24858): (mitochondrial fission factor) This is a nuclear gene encoding a protein that functions in mitochondrial and peroxisomal fission. The encoded protein recruits dynamin-1-like protein (DNM1L) to mitochondria. There are multiple pseudogenes for this gene on chromosomes 1, 5, and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]

MFF links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-227329923-T-TA is Benign according to our data. Variant chr2-227329923-T-TA is described in ClinVar as [Benign]. Clinvar id is 1291453.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFF	NM_001277062.2 linkuse as main transcript	c.-40-692dup		intron_variant		ENST00000304593.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFF	ENST00000304593.14 linkuse as main transcript	c.-40-692dup		intron_variant		2	NM_001277062.2	P1	Q9GZY8-2

Frequencies

GnomAD3 genomes

AF:

0.659

AC:

97891

AN:

148516

Hom.:

32455

Cov.:

show subpopulations

Gnomad AFR

AF:

0.736

Gnomad AMI

AF:

0.709

Gnomad AMR

AF:

0.720

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.756

Gnomad SAS

AF:

0.481

Gnomad FIN

AF:

0.671

Gnomad MID

AF:

0.587

Gnomad NFE

AF:

0.607

Gnomad OTH

AF:

0.664

GnomAD4 exome

AF:

0.483

AC:

125562

AN:

259720

Hom.:

7280

Cov.:

AF XY:

0.483

AC XY:

65767

AN XY:

136302

show subpopulations

Gnomad4 AFR exome

AF:

0.495

Gnomad4 AMR exome

AF:

0.510

Gnomad4 ASJ exome

AF:

0.464

Gnomad4 EAS exome

AF:

0.508

Gnomad4 SAS exome

AF:

0.439

Gnomad4 FIN exome

AF:

0.514

Gnomad4 NFE exome

AF:

0.479

Gnomad4 OTH exome

AF:

0.480

GnomAD4 genome

AF:

0.659

AC:

97941

AN:

148586

Hom.:

32473

Cov.:

AF XY:

0.662

AC XY:

47807

AN XY:

72262

show subpopulations

Gnomad4 AFR

AF:

0.736

Gnomad4 AMR

AF:

0.720

Gnomad4 ASJ

AF:

0.571

Gnomad4 EAS

AF:

0.757

Gnomad4 SAS

AF:

0.482

Gnomad4 FIN

AF:

0.671

Gnomad4 NFE

AF:

0.607

Gnomad4 OTH

AF:

0.667

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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