rs1554091122

Positions:

• chr5-110739253-C-G
• chr5-110739253-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1 PM2 BP4_Moderate

The NM_138773.4(SLC25A46):​c.134C>G​(p.Thr45Ser) 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. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC25A46 NM_138773.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.96

Genes affected

SLC25A46 (HGNC:25198): (solute carrier family 25 member 46) This gene encodes a mitochondrial solute carrier protein family member. It functions in promoting mitochondrial fission, and prevents the formation of hyperfilamentous mitochondria. Mutation of this gene results in neuropathy and optic atrophy. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a modified_residue Phosphothreonine (size 0) in uniprot entity S2546_HUMAN
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.19482982).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A46	NM_138773.4	c.134C>G	p.Thr45Ser	missense_variant	1/8	ENST00000355943.8	NP_620128.1
SLC25A46	NM_001303249.3	c.134C>G	p.Thr45Ser	missense_variant	1/8		NP_001290178.1
SLC25A46	NM_001303250.3	c.10+1006C>G		intron_variant			NP_001290179.1
SLC25A46	NR_138151.2	n.247C>G		non_coding_transcript_exon_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A46	ENST00000355943.8	c.134C>G	p.Thr45Ser	missense_variant	1/8	1	NM_138773.4	ENSP00000348211	P1
SLC25A46	ENST00000447245.6	c.134C>G	p.Thr45Ser	missense_variant	1/8	2		ENSP00000399717
SLC25A46	ENST00000513807.5	c.-204+1006C>G		intron_variant		2		ENSP00000421134
SLC25A46	ENST00000508781.5	n.112+1006C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.013	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	19
DANN	Uncertain	0.98
DEOGEN2	Benign	0.010	T;.
Eigen	Benign	-0.18
Eigen_PC	Benign	-0.057
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.71	T;T
M_CAP	Pathogenic	0.37	D
MetaRNN	Benign	0.19	T;T
MetaSVM	Benign	-0.32	T
MutationAssessor	Benign	1.6	L;L
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.83	D
PROVEAN	Benign	-0.56	N;N
REVEL	Uncertain	0.30
Sift	Benign	0.17	T;T
Sift4G	Benign	0.24	T;T
Polyphen		0.0070	B;.
Vest4		0.14
MutPred		0.16		Gain of sheet (P = 0.0125);Gain of sheet (P = 0.0125);
MVP		0.62
MPC		0.052
ClinPred		0.63	D
GERP RS		3.3
Varity_R		0.15
gMVP		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1554091122; hg19: chr5-110074954;