12-106985067-A-G

Variant names:

• chr12-106985067-A-G
• rs714359
• NM_001033050.3:c.-58+48T>C

Variant summary

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

The NM_001033050.3(MTERF2):​c.-58+48T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,148 control chromosomes in the GnomAD database, including 45,441 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 0.77 (45406 hom., cov: 31)
  • Exomes 𝑓: 0.85 (35 hom.)
• Consequence: MTERF2 NM_001033050.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTERF2	NM_001033050.3	c.-58+48T>C		intron_variant	Intron 2 of 2	ENST00000240050.9	NP_001028222.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTERF2	ENST00000240050.9	c.-58+48T>C		intron_variant	Intron 2 of 2	1	NM_001033050.3	ENSP00000240050.4

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117043 AN: 151942 Hom.: 45360 Cov.: 31

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.786

GnomAD4 exome AF: 0.852 AC: 75 AN: 88 Hom.: 35 Cov.: 0 AF XY: 0.843 AC XY: 59 AN XY: 70

Gnomad4 AFR exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.879

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.770 AC: 117140 AN: 152060 Hom.: 45406 Cov.: 31 AF XY: 0.774 AC XY: 57518 AN XY: 74320

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.788

Alfa AF: 0.785 Hom.: 59634

Bravo AF: 0.774

Asia WGS AF: 0.894 AC: 3107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.084
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs714359; hg19: chr12-107378845;