rs3736032

Variant names:

• chr8-23566184-G-A
• rs3736032
• NM_016612.4:c.287G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-23566184-G-A
• chr8-23566184-G-C
• chr8-23566184-G-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.287G>A​(p.Arg96Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 1,605,314 control chromosomes in the GnomAD database, including 6,617 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.11 (1287 hom., cov: 33)
  • Exomes 𝑓: 0.079 (5330 hom.)
• Consequence: SLC25A37 NM_016612.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 26 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 (MetaRNN=0.0014380515).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016612.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A37	NM_016612.4	MANE Select	c.287G>A	p.Arg96Gln	missense	Exon 2 of 4	NP_057696.2
	SLC25A37	NM_001317813.2		c.71G>A	p.Arg24Gln	missense	Exon 3 of 5	NP_001304742.1
	SLC25A37	NM_001317814.2		c.71G>A	p.Arg24Gln	missense	Exon 3 of 5	NP_001304743.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A37	ENST00000519973.6	TSL:1 MANE Select	c.287G>A	p.Arg96Gln	missense	Exon 2 of 4	ENSP00000429200.1
	SLC25A37	ENST00000290075.10	TSL:1	n.287G>A		non_coding_transcript_exon	Exon 2 of 4	ENSP00000290075.6
	SLC25A37	ENST00000518881.5	TSL:1	n.323G>A		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17163 AN: 152066 Hom.: 1283 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0630

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0803

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.0947

GnomAD2 exomes AF: 0.0889 AC: 21377 AN: 240552 AF XY: 0.0886

Gnomad AFR exome AF: 0.212

Gnomad AMR exome AF: 0.0348

Gnomad ASJ exome AF: 0.0996

Gnomad EAS exome AF: 0.147

Gnomad FIN exome AF: 0.0759

Gnomad NFE exome AF: 0.0700

Gnomad OTH exome AF: 0.0780

GnomAD4 exome AF: 0.0787 AC: 114427 AN: 1453130 Hom.: 5330 Cov.: 51 AF XY: 0.0794 AC XY: 57361 AN XY: 722732

African (AFR) AF: 0.213 AC: 7016 AN: 32976

American (AMR) AF: 0.0386 AC: 1641 AN: 42548

Ashkenazi Jewish (ASJ) AF: 0.0993 AC: 2581 AN: 26004

East Asian (EAS) AF: 0.164 AC: 6424 AN: 39228

South Asian (SAS) AF: 0.124 AC: 10456 AN: 84292

European-Finnish (FIN) AF: 0.0738 AC: 3937 AN: 53338

Middle Eastern (MID) AF: 0.0716 AC: 411 AN: 5738

European-Non Finnish (NFE) AF: 0.0690 AC: 76541 AN: 1108958

Other (OTH) AF: 0.0903 AC: 5420 AN: 60048

GnomAD4 genome AF: 0.113 AC: 17178 AN: 152184 Hom.: 1287 Cov.: 33 AF XY: 0.111 AC XY: 8269 AN XY: 74416

African (AFR) AF: 0.208 AC: 8647 AN: 41504

American (AMR) AF: 0.0629 AC: 962 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3468

East Asian (EAS) AF: 0.155 AC: 803 AN: 5164

South Asian (SAS) AF: 0.129 AC: 624 AN: 4828

European-Finnish (FIN) AF: 0.0803 AC: 851 AN: 10592

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0690 AC: 4692 AN: 68016

Other (OTH) AF: 0.0966 AC: 204 AN: 2112

Alfa AF: 0.0836 Hom.: 2509

Bravo AF: 0.115

TwinsUK AF: 0.0717 AC: 266

ALSPAC AF: 0.0646 AC: 249

ESP6500AA AF: 0.210 AC: 794

ESP6500EA AF: 0.0694 AC: 571

ExAC AF: 0.0937 AC: 11318

Asia WGS AF: 0.159 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.074
BayesDel_addAF	Benign	-0.52	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	18
DANN	Uncertain	1.0
DEOGEN2	Benign	0.16	T
Eigen	Benign	-0.62
Eigen_PC	Benign	-0.59
FATHMM_MKL	Benign	0.28	N
LIST_S2	Uncertain	0.90	D
MetaRNN	Benign	0.0014	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.073
PrimateAI	Benign	0.19	T
PROVEAN	Benign	-1.5	N
REVEL	Benign	0.12
Sift	Benign	0.17	T
Sift4G	Benign	0.18	T
Polyphen		0.055	B
Vest4		0.061
MPC		0.45
ClinPred		0.0028	T
GERP RS		0.22
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.081
gMVP		0.51
Mutation Taster		=97/3	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: rs3736032; hg19: chr8-23423697; COSMIC: COSV107325779; COSMIC: COSV107325779;