GeneBe

NM_138773.4:c.-1G>A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_138773.4(SLC25A46):​c.-1G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,394,390 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.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

SLC25A46
NM_138773.4 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.352

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 -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC25A46NM_138773.4 linkc.-1G>A 5_prime_UTR_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.-1G>A 5_prime_UTR_variant Exon 1 of 8 1 NM_138773.4 ENSP00000348211.3 Q96AG3-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000143
AC:
2
AN:
1394390
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
687852
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
31486
American (AMR)
AF:
0.00
AC:
0
AN:
35624
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25110
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35686
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79124
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
46430
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4604
European-Non Finnish (NFE)
AF:
0.00000185
AC:
2
AN:
1078502
Other (OTH)
AF:
0.00
AC:
0
AN:
57824
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

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
15
DANN
Benign
0.94
PhyloP100
0.35
PromoterAI
-0.013
Neutral

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: rs897837735; hg19: chr5-110074820; COSMIC: COSV100582636; COSMIC: COSV100582636; API