5-151277638-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_181774.4(SLC36A3):c.1168C>T(p.Arg390Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,068 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_181774.4 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC36A3 | NM_181774.4 | c.1168C>T | p.Arg390Cys | missense_variant | 10/10 | ENST00000335230.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC36A3 | ENST00000335230.8 | c.1168C>T | p.Arg390Cys | missense_variant | 10/10 | 1 | NM_181774.4 | P1 | |
SLC36A3 | ENST00000377713.3 | c.1291C>T | p.Arg431Cys | missense_variant | 11/11 | 1 | |||
SLC36A3 | ENST00000423071.2 | n.3068C>T | non_coding_transcript_exon_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250748Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135512
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461798Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727190
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 07, 2022 | The c.1291C>T (p.R431C) alteration is located in exon 11 (coding exon 11) of the SLC36A3 gene. This alteration results from a C to T substitution at nucleotide position 1291, causing the arginine (R) at amino acid position 431 to be replaced by a cysteine (C). 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