chr3-143382098-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_173653.4(SLC9A9):c.1486G>A(p.Asp496Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0013 in 1,614,100 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00065 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 10 hom. )
Consequence
SLC9A9
NM_173653.4 missense
NM_173653.4 missense
Scores
1
4
14
Clinical Significance
Conservation
PhyloP100: 3.67
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 Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010417581).
BP6
?
Variant 3-143382098-C-T is Benign according to our data. Variant chr3-143382098-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 252794.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd at 99 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A9 | NM_173653.4 | c.1486G>A | p.Asp496Asn | missense_variant | 13/16 | ENST00000316549.11 | |
SLC9A9 | XM_017006202.3 | c.1486G>A | p.Asp496Asn | missense_variant | 13/15 | ||
SLC9A9 | XM_017006203.2 | c.1135G>A | p.Asp379Asn | missense_variant | 12/15 | ||
SLC9A9 | XM_011512703.4 | c.838G>A | p.Asp280Asn | missense_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A9 | ENST00000316549.11 | c.1486G>A | p.Asp496Asn | missense_variant | 13/16 | 1 | NM_173653.4 | P1 | |
SLC9A9-AS2 | ENST00000490153.1 | n.264C>T | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000651 AC: 99AN: 152142Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00103 AC: 260AN: 251450Hom.: 3 AF XY: 0.00121 AC XY: 165AN XY: 135892
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GnomAD4 exome AF: 0.00136 AC: 1995AN: 1461840Hom.: 10 Cov.: 31 AF XY: 0.00139 AC XY: 1010AN XY: 727218
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GnomAD4 genome ? AF: 0.000650 AC: 99AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000645 AC XY: 48AN XY: 74456
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Nov 06, 2015 | - - |
Autism, susceptibility to, 16 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 11, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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