rs1956424

chr14-37062697-G-Achr14-37062697-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.70+109584C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,084 control chromosomes in the GnomAD database, including 8,268 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 0.22 (8268 hom., cov: 32)
• Consequence: SLC25A21 NM_030631.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A21	NM_030631.4	c.70+109584C>T		intron_variant		ENST00000331299.6
SLC25A21	NM_001171170.2	c.70+109584C>T		intron_variant
SLC25A21	XM_047431871.1	c.70+109584C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A21	ENST00000331299.6	c.70+109584C>T		intron_variant		1	NM_030631.4	P4
SLC25A21	ENST00000555449.5	c.70+109584C>T		intron_variant		2		A1
SLC25A21	ENST00000557611.1	n.66+109584C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32946 AN: 151966 Hom.: 8237 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.0568

Gnomad FIN AF: 0.0279

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.217 AC: 33025 AN: 152084 Hom.: 8268 Cov.: 32 AF XY: 0.211 AC XY: 15695 AN XY: 74346

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0855

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.0560

Gnomad4 FIN AF: 0.0279

Gnomad4 NFE AF: 0.0470

Gnomad4 OTH AF: 0.175

Alfa AF: 0.0706 Hom.: 2302

Bravo AF: 0.243

Asia WGS AF: 0.159 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.8
Dann	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1956424; hg19: chr14-37531902;