rs10504390

Variant names:

• chr8-65711997-A-G
• rs10504390
• NM_001413073.1:c.933+3986A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001413073.1(MTFR1):​c.933+3986A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0683 in 152,250 control chromosomes in the GnomAD database, including 494 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 0.068 (494 hom., cov: 32)
• Consequence: MTFR1 NM_001413073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 7 publications found

Genes affected

MTFR1 (HGNC:29510): (mitochondrial fission regulator 1) This gene encodes a mitochondrial protein that is characterized by a poly-proline rich region. A chicken homolog of this protein promotes mitochondrial fission and the mouse homolog protects cells from oxidative stress. A related pseudogene of this gene is found on chromosome X. [provided by RefSeq, Mar 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTFR1	NM_001413073.1	c.933+3986A>G		intron_variant	Intron 7 of 8		NP_001400002.1
MTFR1	NM_001413074.1	c.933+3986A>G		intron_variant	Intron 7 of 8		NP_001400003.1
MTFR1	NM_001413075.1	c.933+3986A>G		intron_variant	Intron 7 of 7		NP_001400004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTFR1	ENST00000527155.5	c.372+3986A>G		intron_variant	Intron 2 of 2	3		ENSP00000436928.1
MTFR1	ENST00000521247.6	c.381+3986A>G		intron_variant	Intron 2 of 3	4		ENSP00000429253.2
MTFR1	ENST00000518352.1	n.205+3986A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0683 AC: 10395 AN: 152132 Hom.: 495 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0824

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

GnomAD4 genome AF: 0.0683 AC: 10392 AN: 152250 Hom.: 494 Cov.: 32 AF XY: 0.0659 AC XY: 4904 AN XY: 74440

African (AFR) AF: 0.0186 AC: 774 AN: 41556

American (AMR) AF: 0.0730 AC: 1117 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0483 AC: 233 AN: 4824

European-Finnish (FIN) AF: 0.0619 AC: 656 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7137 AN: 67998

Other (OTH) AF: 0.0810 AC: 171 AN: 2110

Alfa AF: 0.0847 Hom.: 738

Bravo AF: 0.0677

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.63
PhyloP100		-0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10504390; hg19: chr8-66624232;