Variant 2-227327507-A-AAGT 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.-152-1171_-152-1170insAGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.96 ( 70103 hom., cov: 0)

Consequence

MFF
NM_001277062.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0730

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:

MFF (HGNC:):

MFF links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-227327507-A-AAGT is Benign according to our data. Variant chr2-227327507-A-AAGT is described in ClinVar as [Benign]. Clinvar id is 1244076.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MFF	NM_001277062.2 linkuse as main transcript	c.-152-1171_-152-1170insAGT		intron_variant		ENST00000304593.14	NP_001263991.1	Q9GZY8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MFF	ENST00000304593.14 linkuse as main transcript	c.-152-1171_-152-1170insAGT		intron_variant		2	NM_001277062.2	ENSP00000304898.10		Q9GZY8-2

Frequencies

GnomAD3 genomes

AF:

0.958

AC:

145781

AN:

152108

Hom.:

70074

Cov.:

show subpopulations

Gnomad AFR

AF:

0.876

Gnomad AMI

AF:

0.997

Gnomad AMR

AF:

0.980

Gnomad ASJ

AF:

0.972

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.960

Gnomad FIN

AF:

0.999

Gnomad MID

AF:

0.959

Gnomad NFE

AF:

0.993

Gnomad OTH

AF:

0.967

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.958

AC:

145859

AN:

152226

Hom.:

70103

Cov.:

AF XY:

0.959

AC XY:

71362

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.875

Gnomad4 AMR

AF:

0.980

Gnomad4 ASJ

AF:

0.972

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.960

Gnomad4 FIN

AF:

0.999

Gnomad4 NFE

AF:

0.993

Gnomad4 OTH

AF:

0.967

Alfa

AF:

0.979

Hom.:

2734

Bravo

AF:

0.950

Asia WGS

AF:

0.967

AC:

3362

AN:

3476

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

Jun 11, 2018

- -

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