8-23539132-A-G

Variant names:

• chr8-23539132-A-G
• rs7834883
• NM_016612.4:c.210+9920A>G

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+9920A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,114 control chromosomes in the GnomAD database, including 7,169 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 0.23 (7169 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 8 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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+9920A>G		intron	N/A	NP_057696.2	Q9NYZ2-1
	SLC25A37	NM_001317813.2		c.-130-3956A>G		intron	N/A	NP_001304742.1
	SLC25A37	NM_001317814.2		c.-7+2228A>G		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+9920A>G		intron	N/A	ENSP00000429200.1	Q9NYZ2-1
	SLC25A37	ENST00000290075.10	TSL:1	n.210+9920A>G		intron	N/A	ENSP00000290075.6	Q9NYZ2-2
	SLC25A37	ENST00000518881.5	TSL:1	n.246+9920A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35375 AN: 151996 Hom.: 7128 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0817

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.233 AC: 35470 AN: 152114 Hom.: 7169 Cov.: 32 AF XY: 0.233 AC XY: 17298 AN XY: 74368

African (AFR) AF: 0.530 AC: 21956 AN: 41450

American (AMR) AF: 0.186 AC: 2848 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2358 AN: 5154

South Asian (SAS) AF: 0.240 AC: 1159 AN: 4824

European-Finnish (FIN) AF: 0.0672 AC: 712 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0817 AC: 5556 AN: 68016

Other (OTH) AF: 0.191 AC: 403 AN: 2112

Alfa AF: 0.118 Hom.: 987

Bravo AF: 0.251

Asia WGS AF: 0.360 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.25
PhyloP100		-0.43
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: rs7834883; hg19: chr8-23396645;