rs10503725

Variant names:

• chr8-23539024-G-A
• rs10503725
• NM_016612.4:c.210+9812G>A

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+9812G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.05 in 152,238 control chromosomes in the GnomAD database, including 323 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 0.050 (323 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.210+9812G>A		intron_variant	Intron 1 of 3	ENST00000519973.6	NP_057696.2
SLC25A37	NM_001317813.2	c.-130-4064G>A		intron_variant	Intron 1 of 4		NP_001304742.1
SLC25A37	NM_001317814.2	c.-7+2120G>A		intron_variant	Intron 2 of 4		NP_001304743.1
SLC25A37	NM_001317812.2	c.-721+9812G>A		intron_variant	Intron 1 of 3		NP_001304741.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A37	ENST00000519973.6	c.210+9812G>A		intron_variant	Intron 1 of 3	1	NM_016612.4	ENSP00000429200.1

Frequencies

GnomAD3 genomes AF: 0.0500 AC: 7605 AN: 152122 Hom.: 324 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0500 AC: 7617 AN: 152238 Hom.: 323 Cov.: 32 AF XY: 0.0523 AC XY: 3895 AN XY: 74448

African (AFR) AF: 0.0906 AC: 3762 AN: 41534

American (AMR) AF: 0.0980 AC: 1499 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3468

East Asian (EAS) AF: 0.0742 AC: 384 AN: 5178

South Asian (SAS) AF: 0.0542 AC: 261 AN: 4812

European-Finnish (FIN) AF: 0.0248 AC: 263 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0188 AC: 1276 AN: 68020

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.0316 Hom.: 310

Bravo AF: 0.0564

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.75
PhyloP100		-0.034
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs10503725; hg19: chr8-23396537;