chr8-103404817-C-G

Position:

• chr8-103404817-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_030780.5(SLC25A32):​c.350G>C​(p.Arg117Pro) 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. R117H) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC25A32 NM_030780.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

SLC25A32 (HGNC:29683): (solute carrier family 25 member 32) This gene encodes a member of the P(I/L)W subfamily of mitochondrial carrier family transport proteins. The encoded protein transports folate across the inner mitochondrial membrane. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2013]

ENSG00000285982 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.027296335).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A32	NM_030780.5	c.350G>C	p.Arg117Pro	missense_variant	3/7	ENST00000297578.9	NP_110407.2
SLC25A32	NR_102338.2	n.629G>C		non_coding_transcript_exon_variant	4/8
SLC25A32	NR_102337.2	n.476-1493G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A32	ENST00000297578.9	c.350G>C	p.Arg117Pro	missense_variant	3/7	1	NM_030780.5	ENSP00000297578.4
ENSG00000285982	ENST00000649416.1	c.197G>C	p.Arg66Pro	missense_variant	5/9			ENSP00000496817.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	11
DANN	Benign	0.91
DEOGEN2	Benign	0.045	T;.
Eigen	Benign	-1.0
Eigen_PC	Benign	-0.94
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.74	T;T
M_CAP	Benign	0.024	T
MetaRNN	Benign	0.027	T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	-0.61	N;.
PrimateAI	Benign	0.29	T
PROVEAN	Benign	2.3	N;.
REVEL	Benign	0.15
Sift	Benign	0.40	T;.
Sift4G	Benign	0.34	T;.
Polyphen		0.0020	B;.
Vest4		0.15
MutPred		0.26		Loss of solvent accessibility (P = 0.0703);.;
MVP		0.71
MPC		0.45
ClinPred		0.14	T
GERP RS		-2.2
Varity_R		0.088
gMVP		0.79

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-104417045;