rs12821586

Variant names:

• chr12-106986674-G-A
• rs12821586
• ENST00000552029.1:c.-1617C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-106986674-G-A
• chr12-106986674-G-C

Variant summary

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

The ENST00000552029.1(MTERF2):​c.-1617C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0482 in 152,266 control chromosomes in the GnomAD database, including 226 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 0.048 (226 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTERF2 ENST00000552029.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552029.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTERF2	NM_001033050.3	MANE Select	c.-169+295C>T		intron	N/A	NP_001028222.1
	MTERF2	NM_025198.5		c.-159+295C>T		intron	N/A	NP_079474.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTERF2	ENST00000552029.1	TSL:1	c.-1617C>T		5_prime_UTR	Exon 1 of 2	ENSP00000447651.1
	MTERF2	ENST00000240050.9	TSL:1 MANE Select	c.-169+295C>T		intron	N/A	ENSP00000240050.4
	MTERF2	ENST00000392830.6	TSL:1	c.-159+295C>T		intron	N/A	ENSP00000376575.2

Frequencies

GnomAD3 genomes AF: 0.0483 AC: 7342 AN: 152150 Hom.: 226 Cov.: 32

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0353

Gnomad SAS AF: 0.0799

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0411

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 32 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.0482 AC: 7335 AN: 152266 Hom.: 226 Cov.: 32 AF XY: 0.0497 AC XY: 3703 AN XY: 74434

African (AFR) AF: 0.0111 AC: 461 AN: 41564

American (AMR) AF: 0.0269 AC: 412 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3470

East Asian (EAS) AF: 0.0352 AC: 182 AN: 5176

South Asian (SAS) AF: 0.0794 AC: 383 AN: 4826

European-Finnish (FIN) AF: 0.119 AC: 1259 AN: 10592

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4305 AN: 68012

Other (OTH) AF: 0.0421 AC: 89 AN: 2116

Alfa AF: 0.0600 Hom.: 168

Bravo AF: 0.0383

Asia WGS AF: 0.0670 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.55
PhyloP100		0.16
PromoterAI		-0.011	Neutral
Mutation Taster		=100/0	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: rs12821586; hg19: chr12-107380452;