chr5-150010349-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014983.3(HMGXB3):c.551C>T(p.Ala184Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000122 in 1,551,596 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HMGXB3 | NM_014983.3 | c.551C>T | p.Ala184Val | missense_variant | Exon 4 of 20 | ENST00000502717.6 | NP_055798.3 | |
HMGXB3 | XM_047416963.1 | c.551C>T | p.Ala184Val | missense_variant | Exon 4 of 12 | XP_047272919.1 | ||
HMGXB3 | NM_001366501.2 | c.313-1906C>T | intron_variant | Intron 3 of 18 | NP_001353430.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HMGXB3 | ENST00000502717.6 | c.551C>T | p.Ala184Val | missense_variant | Exon 4 of 20 | 1 | NM_014983.3 | ENSP00000421917.1 | ||
HMGXB3 | ENST00000613459.4 | c.1289C>T | p.Ala430Val | missense_variant | Exon 5 of 21 | 5 | ENSP00000479027.1 | |||
HMGXB3 | ENST00000503427.5 | c.551C>T | p.Ala184Val | missense_variant | Exon 4 of 21 | 5 | ENSP00000422231.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000642 AC: 1AN: 155844Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82670
GnomAD4 exome AF: 0.0000129 AC: 18AN: 1399408Hom.: 0 Cov.: 32 AF XY: 0.0000130 AC XY: 9AN XY: 690210
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.551C>T (p.A184V) alteration is located in exon 4 (coding exon 3) of the HMGXB3 gene. This alteration results from a C to T substitution at nucleotide position 551, causing the alanine (A) at amino acid position 184 to be replaced by a valine (V). 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