chr8-23558142-C-T

Variant names:

• chr8-23558142-C-T
• rs11778179
• NM_016612.4:c.211-7966C>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.211-7966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,180 control chromosomes in the GnomAD database, including 2,192 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 0.16 (2192 hom., cov: 33)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.211-7966C>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.211-7966C>T		intron_variant	Intron 1 of 3	1	NM_016612.4	ENSP00000429200.1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24424 AN: 152062 Hom.: 2187 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.161 AC: 24445 AN: 152180 Hom.: 2192 Cov.: 33 AF XY: 0.166 AC XY: 12318 AN XY: 74408

African (AFR) AF: 0.104 AC: 4334 AN: 41530

American (AMR) AF: 0.249 AC: 3807 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3468

East Asian (EAS) AF: 0.161 AC: 834 AN: 5172

South Asian (SAS) AF: 0.188 AC: 910 AN: 4828

European-Finnish (FIN) AF: 0.223 AC: 2362 AN: 10584

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11110 AN: 67988

Other (OTH) AF: 0.170 AC: 360 AN: 2112

Alfa AF: 0.171 Hom.: 366

Bravo AF: 0.158

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.40
DANN	Benign	0.73
PhyloP100		-1.1
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: rs11778179; hg19: chr8-23415655;