rs17698981

chr8-23538588-C-Achr8-23538588-C-T

Variant summary

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

The NM_016612.4(SLC25A37):c.210+9376C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,162 control chromosomes in the GnomAD database, including 1,929 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 0.14 (1929 hom., cov: 31)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.25

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A37	NM_016612.4	c.210+9376C>A		intron_variant		ENST00000519973.6
SLC25A37	NM_001317812.2	c.-721+9376C>A		intron_variant
SLC25A37	NM_001317813.2	c.-130-4500C>A		intron_variant
SLC25A37	NM_001317814.2	c.-7+1684C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A37	ENST00000519973.6	c.210+9376C>A		intron_variant		1	NM_016612.4	P1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21282 AN: 151044 Hom.: 1923 Cov.: 31

Gnomad AFR AF: 0.0365

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.141 AC: 21292 AN: 151162 Hom.: 1929 Cov.: 31 AF XY: 0.145 AC XY: 10698 AN XY: 73810

Gnomad4 AFR AF: 0.0363

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.163

Alfa AF: 0.161 Hom.: 4357

Bravo AF: 0.140

Asia WGS AF: 0.140 AC: 488 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.030
Dann	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs17698981; hg19: chr8-23396101;