5-476619-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_004174.4(SLC9A3):c.1814G>A(p.Arg605Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000212 in 1,609,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004174.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC9A3 | NM_004174.4 | c.1814G>A | p.Arg605Gln | missense_variant | 12/17 | ENST00000264938.8 | NP_004165.2 | |
SLC9A3 | NM_001284351.3 | c.1787G>A | p.Arg596Gln | missense_variant | 12/17 | NP_001271280.1 | ||
SLC9A3-AS1 | NR_125375.1 | n.679+56C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC9A3 | ENST00000264938.8 | c.1814G>A | p.Arg605Gln | missense_variant | 12/17 | 1 | NM_004174.4 | ENSP00000264938.3 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152224Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000267 AC: 66AN: 246780Hom.: 0 AF XY: 0.000261 AC XY: 35AN XY: 134110
GnomAD4 exome AF: 0.000214 AC: 312AN: 1457244Hom.: 0 Cov.: 35 AF XY: 0.000214 AC XY: 155AN XY: 725164
GnomAD4 genome AF: 0.000197 AC: 30AN: 152342Hom.: 0 Cov.: 34 AF XY: 0.000175 AC XY: 13AN XY: 74490
ClinVar
Submissions by phenotype
Congenital secretory sodium diarrhea 8 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 26, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at