dbSNP rs12602832: SLC25A39:c.*473G>A (chr17-44319528-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_001143780.3(SLC25A39):c.*473G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 185,924 control chromosomes in the GnomAD database, including 655 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 0.072 ( 549 hom., cov: 32)

Exomes 𝑓: 0.067 ( 106 hom. )

Consequence

SLC25A39
NM_001143780.3 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.971

Publications

6 publications found

Variant links:

Genes affected

SLC25A39 (HGNC:24279): (solute carrier family 25 member 39) This gene encodes a member of the SLC25 transporter or mitochondrial carrier family of proteins. Members of this family are encoded by the nuclear genome while their protein products are usually embedded in the inner mitochondrial membrane and exhibit wide-ranging substrate specificity. Although the encoded protein is currently considered an orphan transporter, this protein is related to other carriers known to transport amino acids. This protein may play a role in iron homeostasis. [provided by RefSeq, Mar 2016]

SLC25A39 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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001143780.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC25A39	NM_001143780.3	MANE Select	c.*473G>A	downstream_gene	N/A	NP_001137252.1
SLC25A39	NM_001321241.2		c.*473G>A	downstream_gene	N/A	NP_001308170.1
SLC25A39	NM_016016.4		c.*473G>A	downstream_gene	N/A	NP_057100.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC25A39	ENST00000377095.10	TSL:1 MANE Select	c.*473G>A	downstream_gene	N/A	ENSP00000366299.4
SLC25A39	ENST00000225308.12	TSL:1	c.*473G>A	downstream_gene	N/A	ENSP00000225308.8
SLC25A39	ENST00000590194.5	TSL:5	c.*473G>A	downstream_gene	N/A	ENSP00000467681.1

Frequencies

GnomAD3 genomes

AF:

0.0723

AC:

10999

AN:

152154

Hom.:

549

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0192

Gnomad AMI

AF:

0.0319

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.0496

Gnomad EAS

AF:

0.0330

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0881

Gnomad OTH

AF:

0.0817

GnomAD4 exome

AF:

0.0667

AC:

2244

AN:

33652

Hom.:

106

AF XY:

0.0670

AC XY:

1182

AN XY:

17634

show subpopulations

African (AFR)

AF:

0.0142

AC:

AN:

774

American (AMR)

AF:

0.0951

AC:

290

AN:

3048

Ashkenazi Jewish (ASJ)

AF:

0.0368

AC:

AN:

570

East Asian (EAS)

AF:

0.0304

AC:

AN:

1778

South Asian (SAS)

AF:

0.0841

AC:

379

AN:

4506

European-Finnish (FIN)

AF:

0.0883

AC:

103

AN:

1166

Middle Eastern (MID)

AF:

0.0109

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0640

AC:

1280

AN:

20014

Other (OTH)

AF:

0.0616

AC:

105

AN:

1704

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

103

206

309

412

515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome 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

GnomAD4 genome

AF:

0.0722

AC:

10999

AN:

152272

Hom.:

549

Cov.:

AF XY:

0.0752

AC XY:

5596

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.0191

AC:

795

AN:

41566

American (AMR)

AF:

0.114

AC:

1738

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0496

AC:

172

AN:

3470

East Asian (EAS)

AF:

0.0334

AC:

173

AN:

5176

South Asian (SAS)

AF:

0.119

AC:

573

AN:

4828

European-Finnish (FIN)

AF:

0.128

AC:

1354

AN:

10610

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0881

AC:

5993

AN:

68018

Other (OTH)

AF:

0.0799

AC:

169

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

520

1040

1559

2079

2599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<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:

0.0756

Hom.:

706

Bravo

AF:

0.0676

Asia WGS

AF:

0.0800

AC:

280

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.1

(source)

DANN

Benign

0.71

PhyloP100

-0.97

Splicing

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