4-103028859-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178833.7(SLC9B2):āc.1280T>Cā(p.Ile427Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,603,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_178833.7 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 |
---|---|---|---|---|---|---|---|
SLC9B2 | NM_178833.7 | c.1280T>C | p.Ile427Thr | missense_variant | 11/12 | ENST00000394785.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9B2 | ENST00000394785.9 | c.1280T>C | p.Ile427Thr | missense_variant | 11/12 | 2 | NM_178833.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000419 AC: 10AN: 238802Hom.: 0 AF XY: 0.0000462 AC XY: 6AN XY: 129734
GnomAD4 exome AF: 0.000111 AC: 161AN: 1450954Hom.: 0 Cov.: 30 AF XY: 0.000112 AC XY: 81AN XY: 721762
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.1280T>C (p.I427T) alteration is located in exon 11 (coding exon 10) of the SLC9B2 gene. This alteration results from a T to C substitution at nucleotide position 1280, causing the isoleucine (I) at amino acid position 427 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