7-123115555-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022444.4(SLC13A1):c.1751C>T(p.Ser584Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,613,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022444.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC13A1 | NM_022444.4 | c.1751C>T | p.Ser584Leu | missense_variant | 15/15 | ENST00000194130.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC13A1 | ENST00000194130.7 | c.1751C>T | p.Ser584Leu | missense_variant | 15/15 | 1 | NM_022444.4 | P1 | |
SLC13A1 | ENST00000439260.5 | c.*2129C>T | 3_prime_UTR_variant, NMD_transcript_variant | 18/18 | 1 | ||||
SLC13A1 | ENST00000539873.1 | c.*1418C>T | 3_prime_UTR_variant | 16/16 | 5 | ||||
SLC13A1 | ENST00000427975.5 | c.*1694C>T | 3_prime_UTR_variant, NMD_transcript_variant | 16/16 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152096Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250568Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135516
GnomAD4 exome AF: 0.000138 AC: 202AN: 1461262Hom.: 0 Cov.: 30 AF XY: 0.000149 AC XY: 108AN XY: 726930
GnomAD4 genome AF: 0.000164 AC: 25AN: 152096Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.1751C>T (p.S584L) alteration is located in exon 15 (coding exon 15) of the SLC13A1 gene. This alteration results from a C to T substitution at nucleotide position 1751, causing the serine (S) at amino acid position 584 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at