20-5916917-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001819.3(CHGB):c.188C>T(p.Thr63Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,614,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001819.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHGB | ENST00000378961.9 | c.188C>T | p.Thr63Met | missense_variant, splice_region_variant | Exon 3 of 5 | 1 | NM_001819.3 | ENSP00000368244.4 | ||
CHGB | ENST00000455042.1 | c.128C>T | p.Thr43Met | missense_variant, splice_region_variant | Exon 4 of 5 | 3 | ENSP00000416643.1 | |||
CHGB | ENST00000488832.1 | n.967C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251378Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135866
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461762Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727206
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.188C>T (p.T63M) alteration is located in exon 3 (coding exon 3) of the CHGB gene. This alteration results from a C to T substitution at nucleotide position 188, causing the threonine (T) at amino acid position 63 to be replaced by a methionine (M). 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