Variant chr2-227329923-T-TAA 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.-40-693_-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 0.30 ( 7224 hom., cov: 0)

Exomes 𝑓: 0.38 ( 2364 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-TAA is Benign according to our data. Variant chr2-227329923-T-TAA is described in ClinVar as [Benign]. Clinvar id is 1261117.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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.-40-693_-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.-40-693_-40-692dup		intron_variant		2	NM_001277062.2	P1	Q9GZY8-2

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

43907

AN:

148308

Hom.:

7229

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.241

Gnomad SAS

AF:

0.477

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.368

Gnomad NFE

AF:

0.384

Gnomad OTH

AF:

0.299

GnomAD4 exome

AF:

0.377

AC:

93590

AN:

247970

Hom.:

2364

Cov.:

AF XY:

0.377

AC XY:

49079

AN XY:

130134

show subpopulations

Gnomad4 AFR exome

AF:

0.244

Gnomad4 AMR exome

AF:

0.327

Gnomad4 ASJ exome

AF:

0.376

Gnomad4 EAS exome

AF:

0.365

Gnomad4 SAS exome

AF:

0.377

Gnomad4 FIN exome

AF:

0.369

Gnomad4 NFE exome

AF:

0.389

Gnomad4 OTH exome

AF:

0.372

GnomAD4 genome

AF:

0.296

AC:

43889

AN:

148376

Hom.:

7224

Cov.:

AF XY:

0.293

AC XY:

21173

AN XY:

72158

show subpopulations

Gnomad4 AFR

AF:

0.136

Gnomad4 AMR

AF:

0.256

Gnomad4 ASJ

AF:

0.398

Gnomad4 EAS

AF:

0.240

Gnomad4 SAS

AF:

0.476

Gnomad4 FIN

AF:

0.318

Gnomad4 NFE

AF:

0.384

Gnomad4 OTH

AF:

0.296

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

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