14-36784321-T-G

Position:

• chr14-36784321-T-G

Variant summary

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

The ENST00000331299.6(SLC25A21):​c.203+29597A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,232 control chromosomes in the GnomAD database, including 2,290 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 (2290 hom., cov: 32)
• Consequence: SLC25A21 ENST00000331299.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A21	NM_030631.4	c.203+29597A>C		intron_variant		ENST00000331299.6	NP_085134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A21	ENST00000331299.6	c.203+29597A>C		intron_variant		1	NM_030631.4	ENSP00000329452	P4
SLC25A21	ENST00000555449.5	c.203+29597A>C		intron_variant		2		ENSP00000451873	A1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24968 AN: 152114 Hom.: 2288 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.164 AC: 24984 AN: 152232 Hom.: 2290 Cov.: 32 AF XY: 0.164 AC XY: 12177 AN XY: 74430

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.161

Alfa AF: 0.167 Hom.: 1082

Bravo AF: 0.164

Asia WGS AF: 0.193 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.76

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: rs848111; hg19: chr14-37253526;