chr3-179381391-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033540.3(MFN1):​c.1662+2577C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,160 control chromosomes in the GnomAD database, including 38,054 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 0.70 ( 38054 hom., cov: 33)

Consequence

MFN1
NM_033540.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.546
Variant links:
Genes affected
MFN1 (HGNC:18262): (mitofusin 1) The protein encoded by this gene is a mediator of mitochondrial fusion. This protein and mitofusin 2 are homologs of the Drosophila protein fuzzy onion (Fzo). They are mitochondrial membrane proteins that interact with each other to facilitate mitochondrial targeting. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MFN1NM_033540.3 linkc.1662+2577C>A intron_variant Intron 14 of 17 ENST00000471841.6 NP_284941.2 Q8IWA4-1
MFN1XM_005247596.5 linkc.1662+2577C>A intron_variant Intron 14 of 17 XP_005247653.2 Q8IWA4-1
MFN1XM_011512963.4 linkc.1221+2577C>A intron_variant Intron 11 of 14 XP_011511265.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MFN1ENST00000471841.6 linkc.1662+2577C>A intron_variant Intron 14 of 17 1 NM_033540.3 ENSP00000420617.1 Q8IWA4-1

Frequencies

GnomAD3 genomes
AF:
0.703
AC:
106954
AN:
152042
Hom.:
38014
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.787
Gnomad AMI
AF:
0.649
Gnomad AMR
AF:
0.771
Gnomad ASJ
AF:
0.691
Gnomad EAS
AF:
0.654
Gnomad SAS
AF:
0.722
Gnomad FIN
AF:
0.668
Gnomad MID
AF:
0.652
Gnomad NFE
AF:
0.646
Gnomad OTH
AF:
0.716
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.704
AC:
107047
AN:
152160
Hom.:
38054
Cov.:
33
AF XY:
0.706
AC XY:
52535
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.787
Gnomad4 AMR
AF:
0.772
Gnomad4 ASJ
AF:
0.691
Gnomad4 EAS
AF:
0.654
Gnomad4 SAS
AF:
0.720
Gnomad4 FIN
AF:
0.668
Gnomad4 NFE
AF:
0.646
Gnomad4 OTH
AF:
0.720
Alfa
AF:
0.590
Hom.:
1907
Bravo
AF:
0.714
Asia WGS
AF:
0.738
AC:
2564
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.83
DANN
Benign
0.41

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.

Other links and lift over

dbSNP: rs3976523; hg19: chr3-179099179; COSMIC: COSV54938660; COSMIC: COSV54938660; API