rs121912597
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
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
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000022 ( 0 hom. )
Consequence
SLC9A9
NM_173653.4 stop_gained
NM_173653.4 stop_gained
Scores
3
3
1
Clinical Significance
Conservation
PhyloP100: 3.07
Genes affected
SLC9A9 (HGNC:20653): (solute carrier family 9 member A9) This gene encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein family. The encoded protein localizes the to the late recycling endosomes and may play an important role in maintaining cation homeostasis. Mutations in this gene are associated with autism susceptibility 16 and attention-deficit/hyperactivity disorder. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
?
High AC in GnomAd4 at 5 AD gene.
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
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GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251342Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135830
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GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727196
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GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74366
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ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Autism, susceptibility to, 16 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jul 11, 2008 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
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Uncertain
D
MutationTaster
Benign
A
Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at