chr8-65643952-C-T

Variant names:

• chr8-65643952-C-T
• rs10504389
• NM_001413068.1:c.-105C>T

Variant summary

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

The NM_001413068.1(MTFR1):​c.-105C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,074 control chromosomes in the GnomAD database, including 1,232 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 0.12 (1232 hom., cov: 31)
• Consequence: MTFR1 NM_001413068.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445
• Publications: 18 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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTFR1	NM_001413068.1	c.-105C>T		5_prime_UTR_variant	Exon 1 of 8		NP_001399997.1
MTFR1	XM_006716484.3	c.-105C>T		5_prime_UTR_variant	Exon 1 of 8		XP_006716547.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18107 AN: 151956 Hom.: 1229 Cov.: 31

Gnomad AFR AF: 0.0738

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.119 AC: 18116 AN: 152074 Hom.: 1232 Cov.: 31 AF XY: 0.119 AC XY: 8819 AN XY: 74342

African (AFR) AF: 0.0737 AC: 3056 AN: 41482

American (AMR) AF: 0.136 AC: 2074 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3470

East Asian (EAS) AF: 0.0399 AC: 207 AN: 5188

South Asian (SAS) AF: 0.0646 AC: 311 AN: 4814

European-Finnish (FIN) AF: 0.132 AC: 1392 AN: 10546

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9962 AN: 67986

Other (OTH) AF: 0.136 AC: 288 AN: 2114

Alfa AF: 0.137 Hom.: 4958

Bravo AF: 0.118

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.0
DANN	Benign	0.72
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs10504389; hg19: chr8-66556187;