chr5-474893-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004174.4(SLC9A3):āc.2491T>Cā(p.Ser831Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000201 in 1,594,248 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 (ā ).
Frequency
Consequence
NM_004174.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A3 | NM_004174.4 | c.2491T>C | p.Ser831Pro | missense_variant | 16/17 | ENST00000264938.8 | |
SLC9A3-AS1 | NR_125375.1 | n.165-244A>G | intron_variant, non_coding_transcript_variant | ||||
SLC9A3 | NM_001284351.3 | c.2464T>C | p.Ser822Pro | missense_variant | 16/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A3 | ENST00000264938.8 | c.2491T>C | p.Ser831Pro | missense_variant | 16/17 | 1 | NM_004174.4 | P2 | |
SLC9A3-AS1 | ENST00000607286.5 | n.165-244A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000331 AC: 5AN: 151122Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000973 AC: 2AN: 205538Hom.: 0 AF XY: 0.0000178 AC XY: 2AN XY: 112458
GnomAD4 exome AF: 0.0000187 AC: 27AN: 1443126Hom.: 0 Cov.: 43 AF XY: 0.0000209 AC XY: 15AN XY: 716198
GnomAD4 genome AF: 0.0000331 AC: 5AN: 151122Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73782
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 29, 2022 | This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 831 of the SLC9A3 protein (p.Ser831Pro). This variant is present in population databases (rs754007631, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with SLC9A3-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at