3-143268944-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_173653.4(SLC9A9):c.1641G>A(p.Pro547=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00224 in 1,613,366 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 5 hom. )
Consequence
SLC9A9
NM_173653.4 synonymous
NM_173653.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.20
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 -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 3-143268944-C-T is Benign according to our data. Variant chr3-143268944-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 789170.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-143268944-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-5.2 with no splicing effect.
BS2
High AC in GnomAd4 at 187 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A9 | NM_173653.4 | c.1641G>A | p.Pro547= | synonymous_variant | 15/16 | ENST00000316549.11 | |
SLC9A9 | XM_017006203.2 | c.1290G>A | p.Pro430= | synonymous_variant | 14/15 | ||
SLC9A9 | XM_011512703.4 | c.993G>A | p.Pro331= | synonymous_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A9 | ENST00000316549.11 | c.1641G>A | p.Pro547= | synonymous_variant | 15/16 | 1 | NM_173653.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00123 AC: 187AN: 151982Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00109 AC: 275AN: 251382Hom.: 0 AF XY: 0.00120 AC XY: 163AN XY: 135842
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GnomAD4 exome AF: 0.00235 AC: 3431AN: 1461266Hom.: 5 Cov.: 31 AF XY: 0.00232 AC XY: 1684AN XY: 726974
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GnomAD4 genome AF: 0.00123 AC: 187AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.000982 AC XY: 73AN XY: 74356
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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 provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 12, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | SLC9A9: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at