rs2978475

Variant names:

• chr8-23563113-G-A
• rs2978475
• NM_016612.4:c.211-2995G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-23563113-G-A
• chr8-23563113-G-C

Variant summary

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

The NM_016612.4(SLC25A37):​c.211-2995G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,092 control chromosomes in the GnomAD database, including 6,238 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 0.28 (6238 hom., cov: 32)
• Consequence: SLC25A37 NM_016612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A37	NM_016612.4	c.211-2995G>A		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.211-2995G>A		intron_variant	Intron 1 of 3	1	NM_016612.4	ENSP00000429200.1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43014 AN: 151974 Hom.: 6228 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.284

GnomAD3 exomes AF: 0.313 AC: 5 AN: 16 Hom.: 0 AF XY: 0.500 AC XY: 4 AN XY: 8

Gnomad AFR exome AF: 0.00

Gnomad FIN exome AF: 0.500

Gnomad NFE exome AF: 0.333

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

GnomAD4 genome AF: 0.283 AC: 43059 AN: 152092 Hom.: 6238 Cov.: 32 AF XY: 0.280 AC XY: 20785 AN XY: 74320

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.287

Alfa AF: 0.212 Hom.: 605

Bravo AF: 0.291

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2978475; hg19: chr8-23420626;