rs7834536

Variant names:

• chr8-23538915-A-G
• rs7834536
• NM_016612.4:c.210+9703A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016612.4(SLC25A37):​c.210+9703A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,806 control chromosomes in the GnomAD database, including 7,239 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 0.23 (7239 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 8 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016612.4. 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
	SLC25A37	NM_016612.4	MANE Select	c.210+9703A>G		intron	N/A	NP_057696.2	Q9NYZ2-1
	SLC25A37	NM_001317813.2		c.-130-4173A>G		intron	N/A	NP_001304742.1
	SLC25A37	NM_001317814.2		c.-7+2011A>G		intron	N/A	NP_001304743.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A37	ENST00000519973.6	TSL:1 MANE Select	c.210+9703A>G		intron	N/A	ENSP00000429200.1	Q9NYZ2-1
	SLC25A37	ENST00000290075.10	TSL:1	n.210+9703A>G		intron	N/A	ENSP00000290075.6	Q9NYZ2-2
	SLC25A37	ENST00000518881.5	TSL:1	n.246+9703A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35526 AN: 151688 Hom.: 7198 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.0695

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.0676

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.235 AC: 35620 AN: 151806 Hom.: 7239 Cov.: 32 AF XY: 0.234 AC XY: 17394 AN XY: 74192

African (AFR) AF: 0.533 AC: 22051 AN: 41382

American (AMR) AF: 0.188 AC: 2862 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2359 AN: 5122

South Asian (SAS) AF: 0.250 AC: 1201 AN: 4800

European-Finnish (FIN) AF: 0.0676 AC: 712 AN: 10538

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0818 AC: 5556 AN: 67950

Other (OTH) AF: 0.191 AC: 402 AN: 2102

Alfa AF: 0.118 Hom.: 991

Bravo AF: 0.253

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.057
DANN	Benign	0.43
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7834536; hg19: chr8-23396428;