chr8-23540251-C-A

Position:

• chr8-23540251-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016612.4(SLC25A37):​c.210+11039C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0965 in 152,072 control chromosomes in the GnomAD database, including 1,007 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 0.096 (1007 hom., cov: 33)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.210+11039C>A		intron_variant		ENST00000519973.6	NP_057696.2
SLC25A37	NM_001317812.2	c.-721+11039C>A		intron_variant			NP_001304741.1
SLC25A37	NM_001317813.2	c.-130-2837C>A		intron_variant			NP_001304742.1
SLC25A37	NM_001317814.2	c.-7+3347C>A		intron_variant			NP_001304743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A37	ENST00000519973.6	c.210+11039C>A		intron_variant		1	NM_016612.4	ENSP00000429200	P1

Frequencies

GnomAD3 genomes AF: 0.0964 AC: 14653 AN: 151952 Hom.: 1007 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0965 AC: 14674 AN: 152072 Hom.: 1007 Cov.: 33 AF XY: 0.0991 AC XY: 7367 AN XY: 74348

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0485

Gnomad4 NFE AF: 0.0559

Gnomad4 OTH AF: 0.0946

Alfa AF: 0.0294 Hom.: 26

Bravo AF: 0.103

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.13
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs4871881; hg19: chr8-23397764;