rs144851896
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001734.5(C1S):āc.1284C>Gā(p.Pro428=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000681 in 1,614,044 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P428P) has been classified as Likely benign.
Frequency
Consequence
NM_001734.5 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 |
---|---|---|---|---|---|---|---|
C1S | NM_001734.5 | c.1284C>G | p.Pro428= | synonymous_variant | 12/12 | ENST00000360817.10 | |
C1S | NM_201442.4 | c.1284C>G | p.Pro428= | synonymous_variant | 12/12 | ||
C1S | NM_001346850.2 | c.783C>G | p.Pro261= | synonymous_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1S | ENST00000360817.10 | c.1284C>G | p.Pro428= | synonymous_variant | 12/12 | 1 | NM_001734.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000696 AC: 106AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000852 AC: 214AN: 251106Hom.: 0 AF XY: 0.000884 AC XY: 120AN XY: 135796
GnomAD4 exome AF: 0.000679 AC: 993AN: 1461736Hom.: 16 Cov.: 32 AF XY: 0.000696 AC XY: 506AN XY: 727198
GnomAD4 genome AF: 0.000696 AC: 106AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | C1S: BP4, BP7 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Silent variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at