8-23547272-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016612.4(SLC25A37):c.210+18060A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,892 control chromosomes in the GnomAD database, including 10,767 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 0.36 (10767 hom., cov: 31)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

SLC25A37 (HGNC:29786): (solute carrier family 25 member 37) SLC25A37 is a solute carrier localized in the mitochondrial inner membrane. It functions as an essential iron importer for the synthesis of mitochondrial heme and iron-sulfur clusters (summary by Chen et al., 2009 [PubMed 19805291]).[supplied by OMIM, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A37	NM_016612.4	c.210+18060A>G		intron_variant		ENST00000519973.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A37	ENST00000519973.6	c.210+18060A>G		intron_variant		1	NM_016612.4	P1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53952 AN: 151772 Hom.: 10731 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.342

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.356 AC: 54033 AN: 151892 Hom.: 10767 Cov.: 31 AF XY: 0.362 AC XY: 26854 AN XY: 74240

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.343

Alfa AF: 0.276 Hom.: 2698

Bravo AF: 0.369

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	6.3
Dann	Benign	0.55

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

LitVar

Other links and lift over

dbSNP: rs2280861; hg19: chr8-23404785;