chr8-23540251-C-A

Variant names:

• chr8-23540251-C-A
• rs4871881
• NM_016612.4:c.210+11039C>A

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+11039C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0965 in 152,072 control chromosomes in the GnomAD database, including 1,007 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 0.096 (1007 hom., cov: 33)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A37	NM_016612.4	MANE Select	c.210+11039C>A		intron	N/A	NP_057696.2
	SLC25A37	NM_001317813.2		c.-130-2837C>A		intron	N/A	NP_001304742.1
	SLC25A37	NM_001317814.2		c.-7+3347C>A		intron	N/A	NP_001304743.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A37	ENST00000519973.6	TSL:1 MANE Select	c.210+11039C>A		intron	N/A	ENSP00000429200.1
	SLC25A37	ENST00000290075.10	TSL:1	n.210+11039C>A		intron	N/A	ENSP00000290075.6
	SLC25A37	ENST00000518881.5	TSL:1	n.246+11039C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14653 AN: 151952 Hom.: 1007 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0965 AC: 14674 AN: 152072 Hom.: 1007 Cov.: 33 AF XY: 0.0991 AC XY: 7367 AN XY: 74348

African (AFR) AF: 0.134 AC: 5546 AN: 41440

American (AMR) AF: 0.124 AC: 1902 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1793 AN: 5168

South Asian (SAS) AF: 0.122 AC: 590 AN: 4820

European-Finnish (FIN) AF: 0.0485 AC: 513 AN: 10572

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0559 AC: 3801 AN: 67988

Other (OTH) AF: 0.0946 AC: 200 AN: 2114

Alfa AF: 0.0342 Hom.: 35

Bravo AF: 0.103

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.13
DANN	Benign	0.77
PhyloP100		-0.59
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: rs4871881; hg19: chr8-23397764;