rs121912597
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_173653.4(SLC9A9):c.1267C>T(p.Arg423Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_173653.4 stop_gained
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A9 | NM_173653.4 | c.1267C>T | p.Arg423Ter | stop_gained | 11/16 | ENST00000316549.11 | |
SLC9A9 | XM_017006202.3 | c.1267C>T | p.Arg423Ter | stop_gained | 11/15 | ||
SLC9A9 | XM_017006203.2 | c.916C>T | p.Arg306Ter | stop_gained | 10/15 | ||
SLC9A9 | XM_011512703.4 | c.619C>T | p.Arg207Ter | stop_gained | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A9 | ENST00000316549.11 | c.1267C>T | p.Arg423Ter | stop_gained | 11/16 | 1 | NM_173653.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152014Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251342Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135830
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727196
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74366
ClinVar
Submissions by phenotype
Autism, susceptibility to, 16 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jul 11, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at