dbSNP rs7814319: MTERF3:c.488-95G>A (chr8-96251190-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015942.5(MTERF3):c.488-95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 965,494 control chromosomes in the GnomAD database, including 120,840 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 0.56 ( 25953 hom., cov: 32)

Exomes 𝑓: 0.48 ( 94887 hom. )

Consequence

MTERF3
NM_015942.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.762

Publications

7 publications found

Variant links:

Genes affected

MTERF3 (HGNC:24258): (mitochondrial transcription termination factor 3) Enables transcription cis-regulatory region binding activity. Involved in negative regulation of transcription, DNA-templated. Located in cytosol and mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

MTERF3 links:

Genome browser will be placed here

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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MTERF3	NM_015942.5 link	c.488-95G>A	intron_variant	Intron 3 of 7	ENST00000287025.4	NP_057026.3	Q96E29-1
MTERF3	NM_001286643.1 link	c.488-95G>A	intron_variant	Intron 3 of 8		NP_001273572.1	E5RIK9
MTERF3	NM_001362964.1 link	c.-83-95G>A	intron_variant	Intron 3 of 7		NP_001349893.1
MTERF3	XM_011517054.3 link	c.149-95G>A	intron_variant	Intron 3 of 7		XP_011515356.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MTERF3	ENST00000287025.4 link	c.488-95G>A	intron_variant	Intron 3 of 7	1	NM_015942.5	ENSP00000287025.3	Q96E29-1
MTERF3	ENST00000523821.5 link	c.488-95G>A	intron_variant	Intron 3 of 8	1		ENSP00000429400.1	E5RIK9
MTERF3	ENST00000522822.5 link	c.125-95G>A	intron_variant	Intron 1 of 5	2		ENSP00000430138.1	Q96E29-3
MTERF3	ENST00000524341.5 link	c.-83-95G>A	intron_variant	Intron 1 of 4	3		ENSP00000429267.1	E5RIY4

Frequencies

GnomAD3 genomes

AF:

0.558

AC:

84874

AN:

151998

Hom.:

25903

Cov.:

show subpopulations

Gnomad AFR

AF:

0.816

Gnomad AMI

AF:

0.537

Gnomad AMR

AF:

0.410

Gnomad ASJ

AF:

0.511

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.457

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.483

Gnomad OTH

AF:

0.516

GnomAD4 exome

AF:

0.478

AC:

388954

AN:

813378

Hom.:

94887

AF XY:

0.478

AC XY:

197122

AN XY:

412212

show subpopulations

African (AFR)

AF:

0.821

AC:

14067

AN:

17124

American (AMR)

AF:

0.351

AC:

5530

AN:

15748

Ashkenazi Jewish (ASJ)

AF:

0.481

AC:

7691

AN:

15986

East Asian (EAS)

AF:

0.308

AC:

9431

AN:

30638

South Asian (SAS)

AF:

0.484

AC:

22887

AN:

47264

European-Finnish (FIN)

AF:

0.477

AC:

16607

AN:

34808

Middle Eastern (MID)

AF:

0.485

AC:

1488

AN:

3070

European-Non Finnish (NFE)

AF:

0.480

AC:

293360

AN:

611134

Other (OTH)

AF:

0.476

AC:

17893

AN:

37606

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

9909

19818

29728

39637

49546

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7178

14356

21534

28712

35890

<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:

0.559

AC:

84976

AN:

152116

Hom.:

25953

Cov.:

AF XY:

0.552

AC XY:

41077

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.816

AC:

33881

AN:

41524

American (AMR)

AF:

0.410

AC:

6264

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.511

AC:

1773

AN:

3470

East Asian (EAS)

AF:

0.289

AC:

1491

AN:

5166

South Asian (SAS)

AF:

0.456

AC:

2200

AN:

4824

European-Finnish (FIN)

AF:

0.457

AC:

4831

AN:

10566

Middle Eastern (MID)

AF:

0.418

AC:

123

AN:

294

European-Non Finnish (NFE)

AF:

0.483

AC:

32842

AN:

67962

Other (OTH)

AF:

0.512

AC:

1081

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1717

3434

5152

6869

8586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.502

Hom.:

13858

Bravo

AF:

0.561

Asia WGS

AF:

0.397

AC:

1381

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.4

(source)

DANN

Benign

0.66

PhyloP100

-0.76

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over