chr5-474961-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_004174.4(SLC9A3):c.2423G>A(p.Ser808Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000925 in 1,610,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004174.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A3 | NM_004174.4 | c.2423G>A | p.Ser808Asn | missense_variant | 16/17 | ENST00000264938.8 | |
SLC9A3-AS1 | NR_125375.1 | n.165-176C>T | intron_variant, non_coding_transcript_variant | ||||
SLC9A3 | NM_001284351.3 | c.2396G>A | p.Ser799Asn | missense_variant | 16/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A3 | ENST00000264938.8 | c.2423G>A | p.Ser808Asn | missense_variant | 16/17 | 1 | NM_004174.4 | P2 | |
SLC9A3-AS1 | ENST00000607286.5 | n.165-176C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000428 AC: 65AN: 151956Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000117 AC: 28AN: 239146Hom.: 0 AF XY: 0.0000843 AC XY: 11AN XY: 130484
GnomAD4 exome AF: 0.0000576 AC: 84AN: 1458100Hom.: 0 Cov.: 45 AF XY: 0.0000538 AC XY: 39AN XY: 725234
GnomAD4 genome ? AF: 0.000427 AC: 65AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.000417 AC XY: 31AN XY: 74342
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 01, 2022 | This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 808 of the SLC9A3 protein (p.Ser808Asn). This variant is present in population databases (rs201053062, gnomAD 0.2%). 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 output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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