1-205663080-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033102.3(SLC45A3):c.711G>T(p.Leu237Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000895 in 1,452,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033102.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC45A3 | NM_033102.3 | c.711G>T | p.Leu237Phe | missense_variant | 3/5 | ENST00000367145.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC45A3 | ENST00000367145.4 | c.711G>T | p.Leu237Phe | missense_variant | 3/5 | 1 | NM_033102.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000291 AC: 7AN: 240340Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 131016
GnomAD4 exome AF: 0.00000895 AC: 13AN: 1452360Hom.: 0 Cov.: 32 AF XY: 0.00000555 AC XY: 4AN XY: 721120
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.711G>T (p.L237F) alteration is located in exon 3 (coding exon 2) of the SLC45A3 gene. This alteration results from a G to T substitution at nucleotide position 711, causing the leucine (L) at amino acid position 237 to be replaced by a phenylalanine (F). 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