NM_016612.4:c.211-3178T>C

Variant names:

• chr8-23562930-T-C
• rs2928665
• NM_016612.4:c.211-3178T>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.211-3178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,008 control chromosomes in the GnomAD database, including 9,482 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 0.35 (9482 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.21
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.211-3178T>C		intron_variant	Intron 1 of 3	ENST00000519973.6	NP_057696.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A37	ENST00000519973.6	c.211-3178T>C		intron_variant	Intron 1 of 3	1	NM_016612.4	ENSP00000429200.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52694 AN: 151890 Hom.: 9453 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.347 AC: 52778 AN: 152008 Hom.: 9482 Cov.: 32 AF XY: 0.342 AC XY: 25401 AN XY: 74316

African (AFR) AF: 0.427 AC: 17707 AN: 41434

American (AMR) AF: 0.317 AC: 4837 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5154

South Asian (SAS) AF: 0.257 AC: 1237 AN: 4820

European-Finnish (FIN) AF: 0.278 AC: 2942 AN: 10584

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22704 AN: 67962

Other (OTH) AF: 0.349 AC: 737 AN: 2112

Alfa AF: 0.341 Hom.: 4247

Bravo AF: 0.356

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.076
DANN	Benign	0.36
PhyloP100		-5.2
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: rs2928665; hg19: chr8-23420443;