2-171793735-T-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003705.5(SLC25A12):c.1338A>C(p.Pro446Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,614,048 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003705.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A12 | NM_003705.5 | c.1338A>C | p.Pro446Pro | synonymous_variant | Exon 14 of 18 | ENST00000422440.7 | NP_003696.2 | |
SLC25A12 | XM_047446142.1 | c.1065A>C | p.Pro355Pro | synonymous_variant | Exon 12 of 16 | XP_047302098.1 | ||
SLC25A12 | NR_047549.2 | n.1252A>C | non_coding_transcript_exon_variant | Exon 13 of 17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A12 | ENST00000422440.7 | c.1338A>C | p.Pro446Pro | synonymous_variant | Exon 14 of 18 | 1 | NM_003705.5 | ENSP00000388658.2 | ||
SLC25A12 | ENST00000263812.8 | n.*958A>C | non_coding_transcript_exon_variant | Exon 13 of 17 | 2 | ENSP00000263812.4 | ||||
SLC25A12 | ENST00000263812.8 | n.*958A>C | 3_prime_UTR_variant | Exon 13 of 17 | 2 | ENSP00000263812.4 |
Frequencies
GnomAD3 genomes AF: 0.00571 AC: 868AN: 152058Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00181 AC: 456AN: 251250Hom.: 4 AF XY: 0.00137 AC XY: 186AN XY: 135786
GnomAD4 exome AF: 0.000993 AC: 1452AN: 1461872Hom.: 16 Cov.: 32 AF XY: 0.000913 AC XY: 664AN XY: 727234
GnomAD4 genome AF: 0.00570 AC: 868AN: 152176Hom.: 4 Cov.: 32 AF XY: 0.00577 AC XY: 429AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:3
- -
- -
- -
SLC25A12-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at