rs10483481

chr14-36976626-G-C

Variant summary

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

The NM_030631.4(SLC25A21):c.71-101622C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,944 control chromosomes in the GnomAD database, including 18,014 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 0.46 (18014 hom., cov: 31)
• Consequence: SLC25A21 NM_030631.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

Genes affected

SLC25A21 (HGNC:14411): (solute carrier family 25 member 21) SLC25A21 is a homolog of the S. cerevisiae ODC proteins, mitochondrial carriers that transport C5-C7 oxodicarboxylates across inner mitochondrial membranes. One of the species transported by ODC is 2-oxoadipate, a common intermediate in the catabolism of lysine, tryptophan, and hydroxylysine in mammals. Within mitochondria, 2-oxoadipate is converted into acetyl-CoA.[supplied by OMIM, Apr 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A21	NM_030631.4	c.71-101622C>G		intron_variant		ENST00000331299.6
SLC25A21	NM_001171170.2	c.71-101622C>G		intron_variant
SLC25A21	XM_047431871.1	c.71-101622C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A21	ENST00000331299.6	c.71-101622C>G		intron_variant		1	NM_030631.4	P4
SLC25A21	ENST00000555449.5	c.71-101622C>G		intron_variant		2		A1
SLC25A21	ENST00000557611.1	n.67-101622C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70377 AN: 151826 Hom.: 17965 Cov.: 31

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.464 AC: 70482 AN: 151944 Hom.: 18014 Cov.: 31 AF XY: 0.463 AC XY: 34395 AN XY: 74256

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.436

Alfa AF: 0.416 Hom.: 1794

Bravo AF: 0.483

Asia WGS AF: 0.445 AC: 1551 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	12
Dann	Benign	0.73

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: rs10483481; hg19: chr14-37445831;