5-33954406-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000509381.1(SLC45A2):c.661A>C(p.Ser221Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S221G) has been classified as Benign.
Frequency
Consequence
ENST00000509381.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC45A2 | NM_016180.5 | c.987A>C | p.Thr329= | synonymous_variant | 4/7 | ENST00000296589.9 | |
SLC45A2 | NM_001297417.4 | c.661A>C | p.Ser221Arg | missense_variant | 3/4 | ||
SLC45A2 | NM_001012509.4 | c.987A>C | p.Thr329= | synonymous_variant | 4/6 | ||
SLC45A2 | XM_047417259.1 | c.747A>C | p.Thr249= | synonymous_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC45A2 | ENST00000509381.1 | c.661A>C | p.Ser221Arg | missense_variant | 3/4 | 1 | |||
SLC45A2 | ENST00000296589.9 | c.987A>C | p.Thr329= | synonymous_variant | 4/7 | 1 | NM_016180.5 | P1 | |
SLC45A2 | ENST00000382102.7 | c.987A>C | p.Thr329= | synonymous_variant | 4/6 | 1 | |||
SLC45A2 | ENST00000510600.1 | c.462A>C | p.Thr154= | synonymous_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.84e-7 AC: 1AN: 1461738Hom.: 0 Cov.: 67 AF XY: 0.00000138 AC XY: 1AN XY: 727166
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at