rs17089332

chr8-23536227-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+7015C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0242 in 152,268 control chromosomes in the GnomAD database, including 70 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 0.024 (70 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A37	NM_016612.4	c.210+7015C>T		intron_variant		ENST00000519973.6
SLC25A37	NM_001317812.2	c.-721+7015C>T		intron_variant
SLC25A37	NM_001317813.2	c.-130-6861C>T		intron_variant
SLC25A37	NM_001317814.2	c.-77-607C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A37	ENST00000519973.6	c.210+7015C>T		intron_variant		1	NM_016612.4	P1

Frequencies

GnomAD3 genomes AF: 0.0243 AC: 3698 AN: 152150 Hom.: 70 Cov.: 32

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0164

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0930

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0242 AC: 3691 AN: 152268 Hom.: 70 Cov.: 32 AF XY: 0.0243 AC XY: 1809 AN XY: 74460

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.0164

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0165

Alfa AF: 0.0210 Hom.: 36

Bravo AF: 0.0234

Asia WGS AF: 0.0670 AC: 232 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	8.3
Dann	Benign	0.54

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: rs17089332; hg19: chr8-23393740;