rs16963486
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
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 ). 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 -14 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:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at