rs1865855
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_030780.5(SLC25A32):c.391+171T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 151,952 control chromosomes in the GnomAD database, including 1,303 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 1303 hom., cov: 32)
Consequence
SLC25A32
NM_030780.5 intron
NM_030780.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.164
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 8-103404605-A-C is Benign according to our data. Variant chr8-103404605-A-C is described in ClinVar as [Benign]. Clinvar id is 1279525.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A32 | NM_030780.5 | c.391+171T>G | intron_variant | ENST00000297578.9 | |||
SLC25A32 | NR_102337.2 | n.476-1281T>G | intron_variant, non_coding_transcript_variant | ||||
SLC25A32 | NR_102338.2 | n.670+171T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A32 | ENST00000297578.9 | c.391+171T>G | intron_variant | 1 | NM_030780.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.128 AC: 19382AN: 151834Hom.: 1295 Cov.: 32
GnomAD3 genomes
?
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.128 AC: 19412AN: 151952Hom.: 1303 Cov.: 32 AF XY: 0.128 AC XY: 9532AN XY: 74254
GnomAD4 genome
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9532
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74254
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 15, 2019 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at