rs17698981

Variant names:

• chr8-23538588-C-A
• rs17698981
• NM_016612.4:c.210+9376C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-23538588-C-A
• chr8-23538588-C-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+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
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016612.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A37	NM_016612.4	MANE Select	c.210+9376C>A		intron	N/A	NP_057696.2	Q9NYZ2-1
	SLC25A37	NM_001317813.2		c.-130-4500C>A		intron	N/A	NP_001304742.1
	SLC25A37	NM_001317814.2		c.-7+1684C>A		intron	N/A	NP_001304743.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A37	ENST00000519973.6	TSL:1 MANE Select	c.210+9376C>A		intron	N/A	ENSP00000429200.1	Q9NYZ2-1
	SLC25A37	ENST00000290075.10	TSL:1	n.210+9376C>A		intron	N/A	ENSP00000290075.6	Q9NYZ2-2
	SLC25A37	ENST00000518881.5	TSL:1	n.246+9376C>A		intron	N/A

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

African (AFR) AF: 0.0363 AC: 1494 AN: 41106

American (AMR) AF: 0.245 AC: 3704 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3464

East Asian (EAS) AF: 0.157 AC: 801 AN: 5118

South Asian (SAS) AF: 0.174 AC: 829 AN: 4772

European-Finnish (FIN) AF: 0.199 AC: 2073 AN: 10438

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11313 AN: 67854

Other (OTH) AF: 0.163 AC: 341 AN: 2096

Alfa AF: 0.156 Hom.: 6611

Bravo AF: 0.140

Asia WGS AF: 0.140 AC: 488 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.030
DANN	Benign	0.66
PhyloP100		-4.2
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: rs17698981; hg19: chr8-23396101;