chr17-48728264-G-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_006361.6(HOXB13):c.330C>A(p.Pro110=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00154 in 1,614,186 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P110P) has been classified as Likely benign.
Frequency
Consequence
NM_006361.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXB13 | NM_006361.6 | c.330C>A | p.Pro110= | synonymous_variant | 1/2 | ENST00000290295.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXB13 | ENST00000290295.8 | c.330C>A | p.Pro110= | synonymous_variant | 1/2 | 1 | NM_006361.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00635 AC: 966AN: 152216Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00240 AC: 602AN: 251064Hom.: 2 AF XY: 0.00200 AC XY: 272AN XY: 135824
GnomAD4 exome AF: 0.00103 AC: 1511AN: 1461852Hom.: 13 Cov.: 33 AF XY: 0.00103 AC XY: 750AN XY: 727224
GnomAD4 genome ? AF: 0.00640 AC: 975AN: 152334Hom.: 10 Cov.: 32 AF XY: 0.00646 AC XY: 481AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Sep 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jul 20, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Prostate cancer, hereditary, 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2018 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at