rs6022
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_000130.5(F5):c.552G>T(p.Ser184Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,613,178 control chromosomes in the GnomAD database, including 47,929 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. S184S) has been classified as Likely benign.
Frequency
Consequence
NM_000130.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F5 | ENST00000367797.9 | c.552G>T | p.Ser184Ser | synonymous_variant | Exon 4 of 25 | 1 | NM_000130.5 | ENSP00000356771.3 | ||
F5 | ENST00000367796.3 | c.552G>T | p.Ser184Ser | synonymous_variant | Exon 4 of 25 | 5 | ENSP00000356770.3 |
Frequencies
GnomAD3 genomes AF: 0.322 AC: 48902AN: 151662Hom.: 10474 Cov.: 31
GnomAD3 exomes AF: 0.261 AC: 65679AN: 251384Hom.: 11764 AF XY: 0.248 AC XY: 33668AN XY: 135854
GnomAD4 exome AF: 0.202 AC: 294949AN: 1461400Hom.: 37433 Cov.: 35 AF XY: 0.199 AC XY: 144917AN XY: 727034
GnomAD4 genome AF: 0.323 AC: 48970AN: 151778Hom.: 10496 Cov.: 31 AF XY: 0.325 AC XY: 24076AN XY: 74184
ClinVar
Submissions by phenotype
Thrombophilia due to activated protein C resistance Benign:2
- -
- -
not specified Benign:1
- -
Congenital factor V deficiency Benign:1
- -
Budd-Chiari syndrome Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Factor V deficiency Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
- -
Thrombophilia due to thrombin defect Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at