3-143421586-A-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173653.4(SLC9A9):c.1470-39472T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000197 in 151,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Consequence
SLC9A9
NM_173653.4 intron
NM_173653.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.347
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 -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC9A9 | NM_173653.4 | c.1470-39472T>C | intron_variant | ENST00000316549.11 | NP_775924.1 | |||
SLC9A9 | XM_011512703.4 | c.822-39472T>C | intron_variant | XP_011511005.1 | ||||
SLC9A9 | XM_017006202.3 | c.1470-39472T>C | intron_variant | XP_016861691.1 | ||||
SLC9A9 | XM_017006203.2 | c.1119-39472T>C | intron_variant | XP_016861692.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC9A9 | ENST00000316549.11 | c.1470-39472T>C | intron_variant | 1 | NM_173653.4 | ENSP00000320246 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151962Hom.: 0 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151962Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74234
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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