chr1-205659445-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033102.3(SLC45A3):c.1451C>T(p.Pro484Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,613,966 control chromosomes in the GnomAD database, including 1 homozygotes. 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_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.1451C>T | p.Pro484Leu | missense_variant | 5/5 | ENST00000367145.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC45A3 | ENST00000367145.4 | c.1451C>T | p.Pro484Leu | missense_variant | 5/5 | 1 | NM_033102.3 | P1 | |
SLC45A3 | ENST00000460934.1 | n.854C>T | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 40AN: 250766Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135634
GnomAD4 exome AF: 0.000125 AC: 183AN: 1461818Hom.: 1 Cov.: 31 AF XY: 0.000143 AC XY: 104AN XY: 727208
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.1451C>T (p.P484L) alteration is located in exon 5 (coding exon 4) of the SLC45A3 gene. This alteration results from a C to T substitution at nucleotide position 1451, causing the proline (P) at amino acid position 484 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