chr15-50242592-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002112.4(HDC):āc.1657T>Cā(p.Phe553Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00389 in 1,614,148 control chromosomes in the GnomAD database, including 194 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002112.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HDC | NM_002112.4 | c.1657T>C | p.Phe553Leu | missense_variant | 12/12 | ENST00000267845.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HDC | ENST00000267845.8 | c.1657T>C | p.Phe553Leu | missense_variant | 12/12 | 1 | NM_002112.4 | P1 | |
HDC | ENST00000543581.5 | c.1558T>C | p.Phe520Leu | missense_variant | 11/11 | 1 | |||
HDC | ENST00000559816.1 | n.1401T>C | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0206 AC: 3135AN: 152140Hom.: 101 Cov.: 32
GnomAD3 exomes AF: 0.00522 AC: 1312AN: 251482Hom.: 40 AF XY: 0.00391 AC XY: 531AN XY: 135910
GnomAD4 exome AF: 0.00214 AC: 3131AN: 1461890Hom.: 92 Cov.: 33 AF XY: 0.00185 AC XY: 1342AN XY: 727248
GnomAD4 genome AF: 0.0207 AC: 3153AN: 152258Hom.: 102 Cov.: 32 AF XY: 0.0198 AC XY: 1475AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at