rs190788663
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001379110.1(SLC9A6):c.*12C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,204,813 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001379110.1 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A6 | NM_001379110.1 | c.*12C>T | 3_prime_UTR_variant | 18/18 | ENST00000630721.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A6 | ENST00000630721.3 | c.*12C>T | 3_prime_UTR_variant | 18/18 | 4 | NM_001379110.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000107 AC: 12AN: 112103Hom.: 0 Cov.: 22 AF XY: 0.000117 AC XY: 4AN XY: 34267
GnomAD3 exomes AF: 0.0000546 AC: 10AN: 183000Hom.: 0 AF XY: 0.0000592 AC XY: 4AN XY: 67574
GnomAD4 exome AF: 0.0000320 AC: 35AN: 1092655Hom.: 0 Cov.: 29 AF XY: 0.0000363 AC XY: 13AN XY: 358267
GnomAD4 genome ? AF: 0.000107 AC: 12AN: 112158Hom.: 0 Cov.: 22 AF XY: 0.000117 AC XY: 4AN XY: 34332
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 25, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at