8-23554069-T-G

Variant names:

• chr8-23554069-T-G
• rs2978471
• NM_016612.4:c.211-12039T>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.211-12039T>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 151,974 control chromosomes in the GnomAD database, including 17,023 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 (17023 hom., cov: 31)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.211-12039T>G		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.211-12039T>G		intron_variant	Intron 1 of 3	1	NM_016612.4	ENSP00000429200.1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70937 AN: 151858 Hom.: 16999 Cov.: 31

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.467 AC: 71009 AN: 151974 Hom.: 17023 Cov.: 31 AF XY: 0.464 AC XY: 34439 AN XY: 74276

African (AFR) AF: 0.578 AC: 23946 AN: 41414

American (AMR) AF: 0.412 AC: 6290 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1389 AN: 3472

East Asian (EAS) AF: 0.554 AC: 2863 AN: 5164

South Asian (SAS) AF: 0.388 AC: 1867 AN: 4810

European-Finnish (FIN) AF: 0.396 AC: 4187 AN: 10562

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28973 AN: 67966

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.455 Hom.: 2804

Bravo AF: 0.475

Asia WGS AF: 0.476 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.68
PhyloP100		0.0090
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: rs2978471; hg19: chr8-23411582;