8-23552812-C-T

Variant names:

• chr8-23552812-C-T
• rs2928672
• NM_016612.4:c.211-13296C>T

Variant summary

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

The NM_016612.4(SLC25A37):​c.211-13296C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,982 control chromosomes in the GnomAD database, including 14,113 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 0.43 (14113 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.211-13296C>T		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.211-13296C>T		intron_variant	Intron 1 of 3	1	NM_016612.4	ENSP00000429200.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64615 AN: 151864 Hom.: 14098 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.425 AC: 64666 AN: 151982 Hom.: 14113 Cov.: 32 AF XY: 0.423 AC XY: 31384 AN XY: 74266

African (AFR) AF: 0.514 AC: 21294 AN: 41428

American (AMR) AF: 0.388 AC: 5932 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3470

East Asian (EAS) AF: 0.555 AC: 2867 AN: 5168

South Asian (SAS) AF: 0.335 AC: 1613 AN: 4814

European-Finnish (FIN) AF: 0.373 AC: 3927 AN: 10532

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26477 AN: 67976

Other (OTH) AF: 0.417 AC: 880 AN: 2112

Alfa AF: 0.372 Hom.: 5656

Bravo AF: 0.433

Asia WGS AF: 0.453 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs2928672; hg19: chr8-23410325;