NM_152269.5:c.-28-6771A>G

Variant names:

• chr12-123246876-A-G
• rs11532322
• NM_152269.5:c.-28-6771A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152269.5(MTRFR):​c.-28-6771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,438 control chromosomes in the GnomAD database, including 30,590 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 0.59 (30590 hom., cov: 28)
• Consequence: MTRFR NM_152269.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

MTRFR (HGNC:26784): (mitochondrial translation release factor in rescue) This nuclear gene encodes a mitochondrial matrix protein that appears to contribute to peptide chain termination in the mitochondrial translation machinery. Two different 1 bp deletions (resulting in the same premature stop codon)result in decreased mitochondrial translation, decreased levels of oxidative phosphorylation complexes and encepthalomyopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTRFR	NM_152269.5	c.-28-6771A>G		intron_variant	Intron 1 of 2	ENST00000253233.6	NP_689482.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTRFR	ENST00000253233.6	c.-28-6771A>G		intron_variant	Intron 1 of 2	1	NM_152269.5	ENSP00000253233.1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89075 AN: 151322 Hom.: 30590 Cov.: 28

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.588 AC: 89087 AN: 151438 Hom.: 30590 Cov.: 28 AF XY: 0.593 AC XY: 43862 AN XY: 73978

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.618

Alfa AF: 0.554 Hom.: 2056

Bravo AF: 0.561

Asia WGS AF: 0.702 AC: 2439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.21

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

Other links and lift over

dbSNP: rs11532322; hg19: chr12-123731423;