rs1381228940

Variant names:

• chr14-37172332-C-G
• rs1381228940
• NM_030631.4:c.19G>C

Your query was ambiguous. Multiple possible variants found:

• chr14-37172332-C-G
• chr14-37172332-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_030631.4(SLC25A21):​c.19G>C​(p.Val7Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V7I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLC25A21 NM_030631.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

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-AS1 (HGNC:44298): (SLC25A21 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08618379).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A21	NM_030631.4	c.19G>C	p.Val7Leu	missense_variant	Exon 1 of 10	ENST00000331299.6	NP_085134.1
SLC25A21	NM_001171170.2	c.19G>C	p.Val7Leu	missense_variant	Exon 1 of 11		NP_001164641.1
SLC25A21	XM_047431871.1	c.19G>C	p.Val7Leu	missense_variant	Exon 1 of 9		XP_047287827.1
SLC25A21-AS1	NR_033240.1	n.307C>G		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A21	ENST00000331299.6	c.19G>C	p.Val7Leu	missense_variant	Exon 1 of 10	1	NM_030631.4	ENSP00000329452.5
SLC25A21	ENST00000555449.5	c.19G>C	p.Val7Leu	missense_variant	Exon 1 of 11	2		ENSP00000451873.1
SLC25A21-AS1	ENST00000556667.1	n.445C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
SLC25A21	ENST00000557611.1	n.15G>C		non_coding_transcript_exon_variant	Exon 1 of 3	5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	13
DANN	Benign	0.91
DEOGEN2	Benign	0.16	.;T
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.73
FATHMM_MKL	Benign	0.084	N
LIST_S2	Benign	0.50	T;T
M_CAP	Benign	0.023	T
MetaRNN	Benign	0.086	T;T
MetaSVM	Benign	-0.88	T
MutationAssessor	Benign	0.0	N;N
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-0.33	N;N
REVEL	Benign	0.14
Sift	Benign	0.24	T;T
Sift4G	Benign	0.62	T;T
Polyphen		0.0	.;B
Vest4		0.11
MutPred		0.20		Loss of MoRF binding (P = 0.1072);Loss of MoRF binding (P = 0.1072);
MVP		0.60
MPC		0.11
ClinPred		0.095	T
GERP RS		3.4
Varity_R		0.054
gMVP		0.31

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: rs1381228940; hg19: chr14-37641537;