GeneBe

5-110739137-G-C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_138773.4(SLC25A46):​c.18G>C​(p.Pro6Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000716 in 1,396,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P6P) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.2e-7 ( 0 hom. )

Consequence

SLC25A46
NM_138773.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

0 publications found
Variant links:
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]
TMEM232 (HGNC:37270): (transmembrane protein 232) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP7
Synonymous conserved (PhyloP=-1.02 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC25A46NM_138773.4 linkc.18G>C p.Pro6Pro synonymous_variant Exon 1 of 8 ENST00000355943.8 NP_620128.1 Q96AG3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC25A46ENST00000355943.8 linkc.18G>C p.Pro6Pro synonymous_variant Exon 1 of 8 1 NM_138773.4 ENSP00000348211.3 Q96AG3-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.16e-7
AC:
1
AN:
1396170
Hom.:
0
Cov.:
31
AF XY:
0.00000145
AC XY:
1
AN XY:
688656
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
31538
American (AMR)
AF:
0.00
AC:
0
AN:
35664
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25130
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35712
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79162
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
47460
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4936
European-Non Finnish (NFE)
AF:
9.27e-7
AC:
1
AN:
1078692
Other (OTH)
AF:
0.00
AC:
0
AN:
57876
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.36
CADD
Benign
9.3
DANN
Benign
0.88
PhyloP100
-1.0
PromoterAI
-0.026
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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

Other links and lift over

dbSNP: rs1389225741; hg19: chr5-110074838; API