12-106987362-C-G

Variant names:

• chr12-106987362-C-G
• rs2287161
• NM_001033050.3:c.-562G>C

Variant summary

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

The NM_001033050.3(MTERF2):​c.-562G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,996 control chromosomes in the GnomAD database, including 19,525 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 0.50 (19525 hom., cov: 32)
• Consequence: MTERF2 NM_001033050.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 67 publications found

Genes affected

MTERF2 (HGNC:30779): (mitochondrial transcription termination factor 2) Enables DNA binding activity. Predicted to be involved in termination of mitochondrial transcription. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTERF2	NM_001033050.3	c.-562G>C		upstream_gene_variant		ENST00000240050.9	NP_001028222.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTERF2	ENST00000240050.9	c.-562G>C		upstream_gene_variant		1	NM_001033050.3	ENSP00000240050.4

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75745 AN: 151878 Hom.: 19513 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.499 AC: 75795 AN: 151996 Hom.: 19525 Cov.: 32 AF XY: 0.498 AC XY: 37029 AN XY: 74314

African (AFR) AF: 0.416 AC: 17227 AN: 41438

American (AMR) AF: 0.477 AC: 7289 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1442 AN: 3470

East Asian (EAS) AF: 0.855 AC: 4406 AN: 5154

South Asian (SAS) AF: 0.462 AC: 2229 AN: 4822

European-Finnish (FIN) AF: 0.492 AC: 5190 AN: 10554

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36246 AN: 67958

Other (OTH) AF: 0.533 AC: 1123 AN: 2108

Alfa AF: 0.494 Hom.: 2251

Bravo AF: 0.499

Asia WGS AF: 0.653 AC: 2268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		0.40
PromoterAI		0.053	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2287161; hg19: chr12-107381140;