Genetic Variant SLC25A39:c.*473G>A (chr17-44319528-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A39	NM_001143780.3 link	c.*473G>A		downstream_gene_variant		ENST00000377095.10	NP_001137252.1	Q9BZJ4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A39	ENST00000377095.10 link	c.*473G>A		downstream_gene_variant		1	NM_001143780.3	ENSP00000366299.4		Q9BZJ4-1

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

Gnomad4 AFR exome

AF:

0.0142

Gnomad4 AMR exome

AF:

0.0951

Gnomad4 ASJ exome

AF:

0.0368

Gnomad4 EAS exome

AF:

0.0304

Gnomad4 SAS exome

AF:

0.0841

Gnomad4 FIN exome

AF:

0.0883

Gnomad4 NFE exome

AF:

0.0640

Gnomad4 OTH exome

AF:

0.0616

GnomAD4 genome

AF:

0.0722

AC:

10999

AN:

152272

Hom.:

549

Cov.:

AF XY:

0.0752

AC XY:

5596

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0191

Gnomad4 AMR

AF:

0.114

Gnomad4 ASJ

AF:

0.0496

Gnomad4 EAS

AF:

0.0334

Gnomad4 SAS

AF:

0.119

Gnomad4 FIN

AF:

0.128

Gnomad4 NFE

AF:

0.0881

Gnomad4 OTH

AF:

0.0799

Alfa

AF:

0.0777

Hom.:

501

Bravo

AF:

0.0676

Asia WGS

AF:

0.0800

AC:

280

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.1

DANN

Benign

0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over