rs2287162

Positions:

• chr12-106987127-G-C
• chr12-106987127-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MTERF2	NM_001033050.3	c.-327C>G		5_prime_UTR_variant	1/3	ENST00000240050.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTERF2	ENST00000240050.9	c.-327C>G		5_prime_UTR_variant	1/3	1	NM_001033050.3	P1

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

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.817

Gnomad4 OTH exome AF: 0.750

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

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.675

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

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: rs2287162; hg19: chr12-107380905;