4-103047090-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_178833.7(SLC9B2):c.850A>T(p.Thr284Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T284P) has been classified as Uncertain significance.
Frequency
Consequence
NM_178833.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9B2 | NM_178833.7 | c.850A>T | p.Thr284Ser | missense_variant | 7/12 | ENST00000394785.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9B2 | ENST00000394785.9 | c.850A>T | p.Thr284Ser | missense_variant | 7/12 | 2 | NM_178833.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251208Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135756
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461756Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727186
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.850A>T (p.T284S) alteration is located in exon 7 (coding exon 6) of the SLC9B2 gene. This alteration results from a A to T substitution at nucleotide position 850, causing the threonine (T) at amino acid position 284 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at