chr1-173536949-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178527.4(SLC9C2):c.1648C>G(p.Gln550Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,458,752 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178527.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9C2 | NM_178527.4 | c.1648C>G | p.Gln550Glu | missense_variant | 14/28 | ENST00000367714.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9C2 | ENST00000367714.4 | c.1648C>G | p.Gln550Glu | missense_variant | 14/28 | 1 | NM_178527.4 | P1 | |
SLC9C2 | ENST00000466087.1 | n.982C>G | non_coding_transcript_exon_variant | 7/21 | 1 | ||||
SLC9C2 | ENST00000648789.1 | n.572C>G | non_coding_transcript_exon_variant | 5/11 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1458752Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 725886
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2023 | The c.1648C>G (p.Q550E) alteration is located in exon 14 (coding exon 13) of the SLC9C2 gene. This alteration results from a C to G substitution at nucleotide position 1648, causing the glutamine (Q) at amino acid position 550 to be replaced by a glutamic acid (E). 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
Publications
No publications associated with this variant yet.