chr15-50242592-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002112.4(HDC):c.1657T>C(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 (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.021 ( 102 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 92 hom. )
Consequence
HDC
NM_002112.4 missense
NM_002112.4 missense
Scores
1
7
10
Clinical Significance
Conservation
PhyloP100: 6.74
Genes affected
HDC (HGNC:4855): (histidine decarboxylase) This gene encodes a member of the group II decarboxylase family and forms a homodimer that converts L-histidine to histamine in a pyridoxal phosphate dependent manner. Histamine regulates several physiologic processes, including neurotransmission, gastric acid secretion,inflamation, and smooth muscle tone.[provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0043698847).
BP6
?
Variant 15-50242592-A-G is Benign according to our data. Variant chr15-50242592-A-G is described in ClinVar as [Benign]. Clinvar id is 776888.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0709 is higher than 0.05.
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
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GnomAD3 exomes AF: 0.00522 AC: 1312AN: 251482Hom.: 40 AF XY: 0.00391 AC XY: 531AN XY: 135910
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GnomAD4 exome AF: 0.00214 AC: 3131AN: 1461890Hom.: 92 Cov.: 33 AF XY: 0.00185 AC XY: 1342AN XY: 727248
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GnomAD4 genome ? AF: 0.0207 AC: 3153AN: 152258Hom.: 102 Cov.: 32 AF XY: 0.0198 AC XY: 1475AN XY: 74462
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Benign
T;T
Polyphen
D;.
Vest4
MutPred
Gain of helix (P = 0.0325);.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at