8-23538626-C-T

Variant names:

• chr8-23538626-C-T
• rs17089335
• NM_016612.4:c.210+9414C>T

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+9414C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 151,884 control chromosomes in the GnomAD database, including 156 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 0.036 (156 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 2 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.07 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.210+9414C>T		intron_variant	Intron 1 of 3	ENST00000519973.6	NP_057696.2
SLC25A37	NM_001317813.2	c.-130-4462C>T		intron_variant	Intron 1 of 4		NP_001304742.1
SLC25A37	NM_001317814.2	c.-7+1722C>T		intron_variant	Intron 2 of 4		NP_001304743.1
SLC25A37	NM_001317812.2	c.-721+9414C>T		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+9414C>T		intron_variant	Intron 1 of 3	1	NM_016612.4	ENSP00000429200.1

Frequencies

GnomAD3 genomes AF: 0.0362 AC: 5500 AN: 151766 Hom.: 156 Cov.: 32

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0211

Gnomad OTH AF: 0.0192

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

GnomAD4 genome AF: 0.0362 AC: 5505 AN: 151884 Hom.: 156 Cov.: 32 AF XY: 0.0351 AC XY: 2610 AN XY: 74262

African (AFR) AF: 0.0721 AC: 2982 AN: 41334

American (AMR) AF: 0.0185 AC: 282 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3468

East Asian (EAS) AF: 0.0730 AC: 376 AN: 5152

South Asian (SAS) AF: 0.0218 AC: 105 AN: 4808

European-Finnish (FIN) AF: 0.0182 AC: 192 AN: 10576

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0210 AC: 1430 AN: 67982

Other (OTH) AF: 0.0190 AC: 40 AN: 2104

Alfa AF: 0.0278 Hom.: 52

Bravo AF: 0.0380

Asia WGS AF: 0.0520 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		1.3
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: rs17089335; hg19: chr8-23396139;