NM_016612.4:c.211-11843A>G

Variant names:

• chr8-23554265-A-G
• rs2942204
• NM_016612.4:c.211-11843A>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.211-11843A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,016 control chromosomes in the GnomAD database, including 17,003 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 0.47 (17003 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.572 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.211-11843A>G		intron	N/A	NP_057696.2
	SLC25A37	NM_001317813.2		c.-7+11054A>G		intron	N/A	NP_001304742.1
	SLC25A37	NM_001317814.2		c.-6-11843A>G		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.211-11843A>G		intron	N/A	ENSP00000429200.1
	SLC25A37	ENST00000290075.10	TSL:1	n.211-11843A>G		intron	N/A	ENSP00000290075.6
	SLC25A37	ENST00000518881.5	TSL:1	n.247-11843A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70914 AN: 151898 Hom.: 16980 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.467 AC: 70985 AN: 152016 Hom.: 17003 Cov.: 32 AF XY: 0.463 AC XY: 34428 AN XY: 74302

African (AFR) AF: 0.578 AC: 23959 AN: 41436

American (AMR) AF: 0.412 AC: 6291 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2846 AN: 5158

South Asian (SAS) AF: 0.389 AC: 1869 AN: 4810

European-Finnish (FIN) AF: 0.396 AC: 4191 AN: 10576

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.426 AC: 28948 AN: 67978

Other (OTH) AF: 0.453 AC: 956 AN: 2110

Alfa AF: 0.436 Hom.: 6994

Bravo AF: 0.475

Asia WGS AF: 0.476 AC: 1657 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	3.0
DANN	Benign	0.66
PhyloP100		0.13
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: rs2942204; hg19: chr8-23411778;