9-112879775-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033051.4(SLC46A2):c.1415T>C(p.Ile472Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,612,422 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_033051.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC46A2 | NM_033051.4 | c.1415T>C | p.Ile472Thr | missense_variant | Exon 4 of 4 | ENST00000374228.5 | NP_149040.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC46A2 | ENST00000374228.5 | c.1415T>C | p.Ile472Thr | missense_variant | Exon 4 of 4 | 1 | NM_033051.4 | ENSP00000363345.4 | ||
SLC46A2 | ENST00000491462.2 | n.*217T>C | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 | ENSP00000474847.1 | ||||
SNX30 | ENST00000604751.1 | n.3127A>G | non_coding_transcript_exon_variant | Exon 5 of 6 | 2 | |||||
SLC46A2 | ENST00000491462.2 | n.*217T>C | 3_prime_UTR_variant | Exon 4 of 4 | 5 | ENSP00000474847.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251418Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135878
GnomAD4 exome AF: 0.0000425 AC: 62AN: 1460388Hom.: 0 Cov.: 30 AF XY: 0.0000427 AC XY: 31AN XY: 726486
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1415T>C (p.I472T) alteration is located in exon 4 (coding exon 4) of the SLC46A2 gene. This alteration results from a T to C substitution at nucleotide position 1415, causing the isoleucine (I) at amino acid position 472 to be replaced by a threonine (T). 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