rs17089332

Variant names:

• chr8-23536227-C-T
• rs17089332
• NM_016612.4:c.210+7015C>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+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
• 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=-0.81).
• 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 rank	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.210+7015C>T		intron_variant	Intron 1 of 3	ENST00000519973.6	NP_057696.2
SLC25A37	NM_001317813.2	c.-130-6861C>T		intron_variant	Intron 1 of 4		NP_001304742.1
SLC25A37	NM_001317814.2	c.-77-607C>T		intron_variant	Intron 1 of 4		NP_001304743.1
SLC25A37	NM_001317812.2	c.-721+7015C>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+7015C>T		intron_variant	Intron 1 of 3	1	NM_016612.4	ENSP00000429200.1

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

African (AFR) AF: 0.0231 AC: 960 AN: 41542

American (AMR) AF: 0.0164 AC: 251 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3470

East Asian (EAS) AF: 0.0930 AC: 482 AN: 5184

South Asian (SAS) AF: 0.0452 AC: 218 AN: 4818

European-Finnish (FIN) AF: 0.0184 AC: 195 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0215 AC: 1465 AN: 68018

Other (OTH) AF: 0.0165 AC: 35 AN: 2116

Alfa AF: 0.0220 Hom.: 135

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
PhyloP100		0.25
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: rs17089332; hg19: chr8-23393740;