8-23554285-A-C

Variant names:

• chr8-23554285-A-C
• rs7816824
• NM_016612.4:c.211-11823A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016612.4(SLC25A37):​c.211-11823A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 152,258 control chromosomes in the GnomAD database, including 870 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 0.075 (870 hom., cov: 33)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 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.211-11823A>C		intron	N/A	NP_057696.2
	SLC25A37	NM_001317813.2		c.-7+11074A>C		intron	N/A	NP_001304742.1
	SLC25A37	NM_001317814.2		c.-6-11823A>C		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.211-11823A>C		intron	N/A	ENSP00000429200.1
	SLC25A37	ENST00000290075.10	TSL:1	n.211-11823A>C		intron	N/A	ENSP00000290075.6
	SLC25A37	ENST00000518881.5	TSL:1	n.247-11823A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0747 AC: 11361 AN: 152140 Hom.: 868 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0747 AC: 11371 AN: 152258 Hom.: 870 Cov.: 33 AF XY: 0.0777 AC XY: 5787 AN XY: 74460

African (AFR) AF: 0.138 AC: 5738 AN: 41542

American (AMR) AF: 0.110 AC: 1683 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1752 AN: 5158

South Asian (SAS) AF: 0.0645 AC: 311 AN: 4824

European-Finnish (FIN) AF: 0.0250 AC: 266 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0203 AC: 1381 AN: 68026

Other (OTH) AF: 0.0720 AC: 152 AN: 2110

Alfa AF: 0.0399 Hom.: 1481

Bravo AF: 0.0860

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.64
PhyloP100		0.20
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: rs7816824; hg19: chr8-23411798;