chr3-143363560-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_173653.4(SLC9A9):c.1528G>A(p.Ala510Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,460,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173653.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A9 | NM_173653.4 | c.1528G>A | p.Ala510Thr | missense_variant | 14/16 | ENST00000316549.11 | |
SLC9A9 | XM_017006202.3 | c.1528G>A | p.Ala510Thr | missense_variant | 14/15 | ||
SLC9A9 | XM_017006203.2 | c.1177G>A | p.Ala393Thr | missense_variant | 13/15 | ||
SLC9A9 | XM_011512703.4 | c.880G>A | p.Ala294Thr | missense_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A9 | ENST00000316549.11 | c.1528G>A | p.Ala510Thr | missense_variant | 14/16 | 1 | NM_173653.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250794Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135516
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460212Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 726430
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2023 | The c.1528G>A (p.A510T) alteration is located in exon 14 (coding exon 14) of the SLC9A9 gene. This alteration results from a G to A substitution at nucleotide position 1528, causing the alanine (A) at amino acid position 510 to be replaced by a threonine (T). 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