rs2872716

Positions:

• chr8-23540920-A-C
• chr8-23540920-A-G
• chr8-23540920-A-T

Variant summary

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

The NM_016612.4(SLC25A37):​c.210+11708A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,148 control chromosomes in the GnomAD database, including 3,739 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 0.17 (3739 hom., cov: 33)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A37	NM_016612.4	c.210+11708A>C		intron_variant		ENST00000519973.6
SLC25A37	NM_001317812.2	c.-721+11708A>C		intron_variant
SLC25A37	NM_001317813.2	c.-130-2168A>C		intron_variant
SLC25A37	NM_001317814.2	c.-7+4016A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A37	ENST00000519973.6	c.210+11708A>C		intron_variant		1	NM_016612.4	P1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25551 AN: 152030 Hom.: 3729 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0835

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.168 AC: 25603 AN: 152148 Hom.: 3739 Cov.: 33 AF XY: 0.168 AC XY: 12503 AN XY: 74384

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0835

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0485

Gnomad4 NFE AF: 0.0561

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0618 Hom.: 163

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.87
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2872716; hg19: chr8-23398433;