8-23547272-A-G

Variant names:

• chr8-23547272-A-G
• rs2280861
• NM_016612.4:c.210+18060A>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+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
• 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=-0.94).
• 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 rank	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.210+18060A>G		intron_variant	Intron 1 of 3	ENST00000519973.6	NP_057696.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A37	ENST00000519973.6	c.210+18060A>G		intron_variant	Intron 1 of 3	1	NM_016612.4	ENSP00000429200.1

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

African (AFR) AF: 0.497 AC: 20597 AN: 41404

American (AMR) AF: 0.427 AC: 6522 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3468

East Asian (EAS) AF: 0.615 AC: 3161 AN: 5142

South Asian (SAS) AF: 0.423 AC: 2036 AN: 4808

European-Finnish (FIN) AF: 0.276 AC: 2911 AN: 10552

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16882 AN: 67946

Other (OTH) AF: 0.343 AC: 724 AN: 2108

Alfa AF: 0.273 Hom.: 2957

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
PhyloP100		-0.10
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: rs2280861; hg19: chr8-23404785;