5-150010268-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014983.3(HMGXB3):c.470C>A(p.Ser157Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000214 in 1,399,516 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014983.3 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 |
---|---|---|---|---|---|---|---|
HMGXB3 | NM_014983.3 | c.470C>A | p.Ser157Tyr | missense_variant | 4/20 | ENST00000502717.6 | |
HMGXB3 | XM_047416963.1 | c.470C>A | p.Ser157Tyr | missense_variant | 4/12 | ||
HMGXB3 | NM_001366501.2 | c.313-1987C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMGXB3 | ENST00000502717.6 | c.470C>A | p.Ser157Tyr | missense_variant | 4/20 | 1 | NM_014983.3 | P2 | |
HMGXB3 | ENST00000613459.4 | c.1208C>A | p.Ser403Tyr | missense_variant | 5/21 | 5 | A2 | ||
HMGXB3 | ENST00000503427.5 | c.470C>A | p.Ser157Tyr | missense_variant | 4/21 | 5 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1399516Hom.: 0 Cov.: 32 AF XY: 0.00000435 AC XY: 3AN XY: 690256
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2023 | The c.470C>A (p.S157Y) alteration is located in exon 4 (coding exon 3) of the HMGXB3 gene. This alteration results from a C to A substitution at nucleotide position 470, causing the serine (S) at amino acid position 157 to be replaced by a tyrosine (Y). 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