rs3749779

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_031947.4(SLC25A2):c.542T>G(p.Val181Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,614,202 control chromosomes in the GnomAD database, including 1,153 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 0.017 ( 137 hom., cov: 32)

Exomes 𝑓: 0.012 ( 1016 hom. )

Consequence

SLC25A2
NM_031947.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.77

Publications

15 publications found

Variant links:

Genes affected

SLC25A2 (HGNC:22921): (solute carrier family 25 member 2) This intronless gene encodes a protein that localizes to the mitochondrial inner membrane and likely functions as a transporter of small molecules such as ornithine. This gene is located between the protocadherin beta and gamma gene clusters on chromosome 5. [provided by RefSeq, Dec 2014]

SLC25A2 links:

TAF7 (HGNC:11541): (TATA-box binding protein associated factor 7) The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. [provided by RefSeq, Jul 2008]

TAF7 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_031947.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.0024497807).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0996 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031947.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A2	NM_031947.4	MANE Select	c.542T>G	p.Val181Gly	missense	Exon 1 of 1	NP_114153.1	Q9BXI2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC25A2	ENST00000239451.7	TSL:6 MANE Select	c.542T>G	p.Val181Gly	missense	Exon 1 of 1	ENSP00000239451.4	Q9BXI2
TAF7	ENST00000624699.1	TSL:3	n.128+17194T>G		intron	N/A
TAF7	ENST00000686518.1		n.75+17194T>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0172

AC:

2617

AN:

152202

Hom.:

133

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00359

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.0378

Gnomad FIN

AF:

0.00301

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00173

Gnomad OTH

AF:

0.0134

GnomAD2 exomes

AF:

0.0382

AC:

9604

AN:

251392

AF XY:

0.0331

show subpopulations

Gnomad AFR exome

AF:

0.00326

Gnomad AMR exome

AF:

0.177

Gnomad ASJ exome

AF:

0.000893

Gnomad EAS exome

AF:

0.0952

Gnomad FIN exome

AF:

0.00388

Gnomad NFE exome

AF:

0.00208

Gnomad OTH exome

AF:

0.0262

GnomAD4 exome

AF:

0.0118

AC:

17310

AN:

1461882

Hom.:

1016

Cov.:

AF XY:

0.0119

AC XY:

8681

AN XY:

727242

show subpopulations

African (AFR)

AF:

0.00278

AC:

AN:

33480

American (AMR)

AF:

0.167

AC:

7474

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.000957

AC:

AN:

26132

East Asian (EAS)

AF:

0.0944

AC:

3746

AN:

39700

South Asian (SAS)

AF:

0.0378

AC:

3259

AN:

86258

European-Finnish (FIN)

AF:

0.00348

AC:

186

AN:

53412

Middle Eastern (MID)

AF:

0.00260

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00156

AC:

1732

AN:

1112012

Other (OTH)

AF:

0.0129

AC:

780

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1077

2154

3232

4309

5386

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.0173

AC:

2634

AN:

152320

Hom.:

137

Cov.:

AF XY:

0.0200

AC XY:

1489

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.00361

AC:

150

AN:

41580

American (AMR)

AF:

0.104

AC:

1588

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00144

AC:

AN:

3472

East Asian (EAS)

AF:

0.102

AC:

526

AN:

5178

South Asian (SAS)

AF:

0.0379

AC:

183

AN:

4832

European-Finnish (FIN)

AF:

0.00301

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00173

AC:

118

AN:

68032

Other (OTH)

AF:

0.0132

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

112

223

335

446

558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

140

<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:

0.00905

Hom.:

193

Bravo

AF:

0.0258

Asia WGS

AF:

0.0650

AC:

224

AN:

3478

EpiCase

AF:

0.00131

EpiControl

AF:

0.00190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.40

BayesDel_addAF

Benign

-0.29

BayesDel_noAF

Uncertain

-0.040

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.42

Eigen

Uncertain

0.43

Eigen_PC

Uncertain

0.38

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.86

MetaRNN

Benign

0.0024

MetaSVM

Benign

-0.87

MutationAssessor

Benign

1.8

PhyloP100

7.8

PrimateAI

Benign

0.37

PROVEAN

Pathogenic

-5.1

REVEL

Uncertain

0.56

Sift

Uncertain

0.0010

Sift4G

Pathogenic

0.0

Varity_R

0.78

gMVP

0.31

Mutation Taster

=92/8

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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