17-18969052-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001042450.4(SLC5A10):c.454C>A(p.Leu152Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001042450.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC5A10 | NM_001042450.4 | c.454C>A | p.Leu152Met | missense_variant, splice_region_variant | Exon 6 of 15 | ENST00000395645.4 | NP_001035915.1 | |
FAM83G | NM_001039999.3 | c.*2307G>T | 3_prime_UTR_variant | Exon 6 of 6 | ENST00000388995.11 | NP_001035088.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A10 | ENST00000395645.4 | c.454C>A | p.Leu152Met | missense_variant, splice_region_variant | Exon 6 of 15 | 1 | NM_001042450.4 | ENSP00000379007.3 | ||
FAM83G | ENST00000388995 | c.*2307G>T | 3_prime_UTR_variant | Exon 6 of 6 | 5 | NM_001039999.3 | ENSP00000373647.5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460422Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726490
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.454C>A (p.L152M) alteration is located in exon 6 (coding exon 6) of the SLC5A10 gene. This alteration results from a C to A substitution at nucleotide position 454, causing the leucine (L) at amino acid position 152 to be replaced by a methionine (M). 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
Publications
No publications associated with this variant yet.