Genetic Variant MTERF1:c.*501G>C (chr7-91873093-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006980.5(MTERF1):c.*501G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,230 control chromosomes in the GnomAD database, including 14,868 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 0.43 ( 14832 hom., cov: 32)

Exomes 𝑓: 0.53 ( 36 hom. )

Consequence

MTERF1
NM_006980.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

Publications

7 publications found

Variant links:

Genes affected

MTERF1 (HGNC:21463): (mitochondrial transcription termination factor 1) This gene encodes a mitochondrial transcription termination factor. This protein participates in attenuating transcription from the mitochondrial genome; this attenuation allows higher levels of expression of 16S ribosomal RNA relative to the tRNA gene downstream. The product of this gene has three leucine zipper motifs bracketed by two basic domains that are all required for DNA binding. There is evidence that, for this protein, the zippers participate in intramolecular interactions that establish the three-dimensional structure required for DNA binding. [provided by RefSeq, Jul 2008]

MTERF1 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006980.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MTERF1	NM_006980.5	MANE Select	c.*501G>C	3_prime_UTR	Exon 3 of 3	NP_008911.1
MTERF1	NM_001301134.2		c.*501G>C	3_prime_UTR	Exon 2 of 2	NP_001288063.1
MTERF1	NM_001301135.2		c.*501G>C	3_prime_UTR	Exon 4 of 4	NP_001288064.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MTERF1	ENST00000351870.8	TSL:1 MANE Select	c.*501G>C	3_prime_UTR	Exon 3 of 3	ENSP00000248643.3
MTERF1	ENST00000419292.1	TSL:1	c.*501G>C	3_prime_UTR	Exon 2 of 2	ENSP00000414116.1
MTERF1	ENST00000454222.5	TSL:5	n.93+6962G>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64716

AN:

151892

Hom.:

14825

Cov.:

show subpopulations

Gnomad AFR

AF:

0.241

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.518

Gnomad ASJ

AF:

0.353

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.447

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.504

Gnomad OTH

AF:

0.430

GnomAD4 exome

AF:

0.532

AC:

117

AN:

220

Hom.:

Cov.:

AF XY:

0.566

AC XY:

AN XY:

122

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.100

AC:

AN:

East Asian (EAS)

AF:

0.833

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.563

AC:

AN:

158

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.426

AC:

64729

AN:

152010

Hom.:

14832

Cov.:

AF XY:

0.427

AC XY:

31699

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.241

AC:

9982

AN:

41478

American (AMR)

AF:

0.518

AC:

7915

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.353

AC:

1224

AN:

3472

East Asian (EAS)

AF:

0.436

AC:

2257

AN:

5178

South Asian (SAS)

AF:

0.446

AC:

2148

AN:

4820

European-Finnish (FIN)

AF:

0.507

AC:

5354

AN:

10550

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.504

AC:

34234

AN:

67926

Other (OTH)

AF:

0.431

AC:

910

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1830

3660

5491

7321

9151

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

606

1212

1818

2424

3030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.321

Hom.:

891

Bravo

AF:

0.419

Asia WGS

AF:

0.443

AC:

1537

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.61

(source)

DANN

Benign

0.74

PhyloP100

0.031

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over