8-23540722-C-G

Variant names:

• chr8-23540722-C-G
• rs7826247
• NM_016612.4:c.210+11510C>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+11510C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,960 control chromosomes in the GnomAD database, including 12,696 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 0.38 (12696 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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+11510C>G		intron	N/A	NP_057696.2	Q9NYZ2-1
	SLC25A37	NM_001317813.2		c.-130-2366C>G		intron	N/A	NP_001304742.1
	SLC25A37	NM_001317814.2		c.-7+3818C>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+11510C>G		intron	N/A	ENSP00000429200.1	Q9NYZ2-1
	SLC25A37	ENST00000290075.10	TSL:1	n.210+11510C>G		intron	N/A	ENSP00000290075.6	Q9NYZ2-2
	SLC25A37	ENST00000518881.5	TSL:1	n.246+11510C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58022 AN: 151844 Hom.: 12657 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.382 AC: 58113 AN: 151960 Hom.: 12696 Cov.: 32 AF XY: 0.388 AC XY: 28804 AN XY: 74274

African (AFR) AF: 0.569 AC: 23563 AN: 41416

American (AMR) AF: 0.437 AC: 6666 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3466

East Asian (EAS) AF: 0.615 AC: 3178 AN: 5168

South Asian (SAS) AF: 0.423 AC: 2038 AN: 4816

European-Finnish (FIN) AF: 0.304 AC: 3216 AN: 10568

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17428 AN: 67944

Other (OTH) AF: 0.361 AC: 760 AN: 2108

Alfa AF: 0.167 Hom.: 319

Bravo AF: 0.397

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		0.29
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: rs7826247; hg19: chr8-23398235;