14-36742361-T-C

Position:

• chr14-36742361-T-C

Variant summary

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

The NM_030631.4(SLC25A21):​c.204-7788A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,998 control chromosomes in the GnomAD database, including 26,028 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 0.57 (26028 hom., cov: 32)
• Consequence: SLC25A21 NM_030631.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

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]

SLC25A21 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A21	NM_030631.4	c.204-7788A>G		intron_variant		ENST00000331299.6	NP_085134.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A21	ENST00000331299.6	c.204-7788A>G		intron_variant		1	NM_030631.4	ENSP00000329452.5
SLC25A21	ENST00000555449.5	c.204-7788A>G		intron_variant		2		ENSP00000451873.1
SLC25A21	ENST00000546428.2	n.70-7788A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86484 AN: 151880 Hom.: 25983 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.570 AC: 86587 AN: 151998 Hom.: 26028 Cov.: 32 AF XY: 0.566 AC XY: 42051 AN XY: 74298

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.537

Alfa AF: 0.512 Hom.: 25927

Bravo AF: 0.570

Asia WGS AF: 0.487 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.9
DANN	Benign	0.45

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: rs1033594; hg19: chr14-37211566;