3-125107489-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024628.6(SLC12A8):c.1697G>A(p.Ser566Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,606,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024628.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A8 | NM_024628.6 | c.1697G>A | p.Ser566Asn | missense_variant | 10/14 | ENST00000469902.6 | |
SLC12A8 | NM_001195483.2 | c.1697G>A | p.Ser566Asn | missense_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A8 | ENST00000469902.6 | c.1697G>A | p.Ser566Asn | missense_variant | 10/14 | 2 | NM_024628.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000604 AC: 15AN: 248248Hom.: 0 AF XY: 0.0000520 AC XY: 7AN XY: 134606
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1453774Hom.: 0 Cov.: 32 AF XY: 0.0000111 AC XY: 8AN XY: 721336
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.1697G>A (p.S566N) alteration is located in exon 10 (coding exon 9) of the SLC12A8 gene. This alteration results from a G to A substitution at nucleotide position 1697, causing the serine (S) at amino acid position 566 to be replaced by an asparagine (N). 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