12-106987127-G-C

Variant names:

• chr12-106987127-G-C
• rs2287162
• NM_001033050.3:c.-327C>G

Variant summary

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

The NM_001033050.3(MTERF2):​c.-327C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,222 control chromosomes in the GnomAD database, including 33,886 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 0.66 (33857 hom., cov: 33)
  • Exomes 𝑓: 0.80 (29 hom.)
• Consequence: MTERF2 NM_001033050.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 8 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTERF2	NM_001033050.3	c.-327C>G		5_prime_UTR_variant	Exon 1 of 3	ENST00000240050.9	NP_001028222.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTERF2	ENST00000240050.9	c.-327C>G		5_prime_UTR_variant	Exon 1 of 3	1	NM_001033050.3	ENSP00000240050.4

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100123 AN: 152008 Hom.: 33829 Cov.: 33

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.676

GnomAD4 exome AF: 0.802 AC: 77 AN: 96 Hom.: 29 Cov.: 0 AF XY: 0.828 AC XY: 53 AN XY: 64

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.817 AC: 67 AN: 82

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.659 AC: 100201 AN: 152126 Hom.: 33857 Cov.: 33 AF XY: 0.657 AC XY: 48890 AN XY: 74360

African (AFR) AF: 0.497 AC: 20614 AN: 41486

American (AMR) AF: 0.707 AC: 10810 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1997 AN: 3470

East Asian (EAS) AF: 0.748 AC: 3850 AN: 5144

South Asian (SAS) AF: 0.658 AC: 3175 AN: 4826

European-Finnish (FIN) AF: 0.685 AC: 7254 AN: 10596

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50336 AN: 67990

Other (OTH) AF: 0.675 AC: 1424 AN: 2110

Alfa AF: 0.615 Hom.: 2061

Bravo AF: 0.657

Asia WGS AF: 0.685 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.54
PhyloP100		-1.2
PromoterAI		-0.070	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2287162; hg19: chr12-107380905;