15-77477576-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001304504.2(HMG20A):c.637C>T(p.Arg213Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000343 in 1,458,782 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R213Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001304504.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HMG20A | ENST00000336216.9 | c.637C>T | p.Arg213Trp | missense_variant | Exon 7 of 10 | 1 | NM_001304504.2 | ENSP00000336856.4 | ||
HMG20A | ENST00000381714.7 | c.637C>T | p.Arg213Trp | missense_variant | Exon 8 of 11 | 1 | ENSP00000371133.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250466Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135400
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458782Hom.: 0 Cov.: 28 AF XY: 0.00000275 AC XY: 2AN XY: 725956
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.637C>T (p.R213W) alteration is located in exon 8 (coding exon 6) of the HMG20A gene. This alteration results from a C to T substitution at nucleotide position 637, causing the arginine (R) at amino acid position 213 to be replaced by a tryptophan (W). 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