NM_000071.3:c.297C>T
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000071.3(CBS):c.297C>T(p.Phe99Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000071.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- classic homocystinuriaInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Myriad Women’s Health, PanelApp Australia, ClinGen, Genomics England PanelApp
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ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000258 AC: 1AN: 38818Hom.: 0 Cov.: 6 show subpopulations
GnomAD2 exomes AF: 0.0000199 AC: 5AN: 251346 AF XY: 0.0000294 show subpopulations
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000149 AC: 5AN: 336350Hom.: 0 Cov.: 0 AF XY: 0.0000110 AC XY: 2AN XY: 181038 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
Age Distribution
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000257 AC: 1AN: 38906Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 17816 show subpopulations
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
This alteration is classified as likely 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. -
HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at