rs782529317
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001379110.1(SLC9A6):āc.228T>Cā(p.Asn76=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,209,666 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001379110.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.228T>C | p.Asn76= | synonymous_variant | 3/18 | ENST00000630721.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.228T>C | p.Asn76= | synonymous_variant | 3/18 | 4 | NM_001379110.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000537 AC: 6AN: 111732Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33900
GnomAD3 exomes AF: 0.0000599 AC: 11AN: 183515Hom.: 0 AF XY: 0.0000589 AC XY: 4AN XY: 67943
GnomAD4 exome AF: 0.0000355 AC: 39AN: 1097934Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 13AN XY: 363298
GnomAD4 genome ? AF: 0.0000537 AC: 6AN: 111732Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33900
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Christianson syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at