3-120628437-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_000187.4(HGD):c.1281G>A(p.Trp427Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000187.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGD | NM_000187.4 | c.1281G>A | p.Trp427Ter | stop_gained | 14/14 | ENST00000283871.10 | |
HGD | XM_005247412.3 | c.1056G>A | p.Trp352Ter | stop_gained | 12/12 | ||
HGD | XM_017006277.3 | c.858G>A | p.Trp286Ter | stop_gained | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGD | ENST00000283871.10 | c.1281G>A | p.Trp427Ter | stop_gained | 14/14 | 1 | NM_000187.4 | P1 | |
HGD | ENST00000492108.5 | c.*263G>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461814Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727230
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Alkaptonuria Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | 3billion | - | The variant is not observed in the gnomAD v2.1.1 dataset. The variant is predicted to result in a loss or disruption of normal protein function through protein truncation. The predicted truncated protein may be shortened by less than 10%. The evidence of pathogenicity is insufficient at this time.Therefore, this variant is classified as Uncertain significance according to the recommendation of ACMG/AMP guideline. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.