5-110738696-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001303250.3(SLC25A46):c.10+449T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 228,832 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.023 ( 43 hom., cov: 32)
Exomes 𝑓: 0.015 ( 17 hom. )
Consequence
SLC25A46
NM_001303250.3 intron
NM_001303250.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0750
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 5-110738696-T-C is Benign according to our data. Variant chr5-110738696-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1219661.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0231 (3509/151998) while in subpopulation AFR AF= 0.0283 (1175/41488). AF 95% confidence interval is 0.027. There are 43 homozygotes in gnomad4. There are 1706 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 43 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A46 | NM_001303250.3 | c.10+449T>C | intron_variant | ||||
TMEM232 | XM_006714670.4 | c.-298+26A>G | intron_variant | ||||
TMEM232 | XM_011543552.3 | c.-649+26A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A46 | ENST00000513807.5 | c.-204+449T>C | intron_variant | 2 | |||||
TMEM232 | ENST00000515278.6 | c.-298+26A>G | intron_variant | 5 | |||||
TMEM232 | ENST00000503527.6 | n.197+26A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
SLC25A46 | ENST00000508781.5 | n.112+449T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0231 AC: 3509AN: 151878Hom.: 43 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
3509
AN:
151878
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0149 AC: 1144AN: 76834Hom.: 17 Cov.: 0 AF XY: 0.0139 AC XY: 565AN XY: 40686
GnomAD4 exome
AF:
AC:
1144
AN:
76834
Hom.:
Cov.:
0
AF XY:
AC XY:
565
AN XY:
40686
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0231 AC: 3509AN: 151998Hom.: 43 Cov.: 32 AF XY: 0.0230 AC XY: 1706AN XY: 74276
GnomAD4 genome
?
AF:
AC:
3509
AN:
151998
Hom.:
Cov.:
32
AF XY:
AC XY:
1706
AN XY:
74276
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
31
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 07, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at