rs6021
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000130.5(F5):c.2301A>G(p.Ser767Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,613,850 control chromosomes in the GnomAD database, including 60,148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000130.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F5 | ENST00000367797.9 | c.2301A>G | p.Ser767Ser | synonymous_variant | Exon 13 of 25 | 1 | NM_000130.5 | ENSP00000356771.3 | ||
F5 | ENST00000367796.3 | c.2316A>G | p.Ser772Ser | synonymous_variant | Exon 13 of 25 | 5 | ENSP00000356770.3 |
Frequencies
GnomAD3 genomes AF: 0.245 AC: 37285AN: 152018Hom.: 4745 Cov.: 32
GnomAD3 exomes AF: 0.278 AC: 69942AN: 251178Hom.: 10548 AF XY: 0.278 AC XY: 37777AN XY: 135746
GnomAD4 exome AF: 0.272 AC: 397369AN: 1461716Hom.: 55392 Cov.: 45 AF XY: 0.273 AC XY: 198335AN XY: 727168
GnomAD4 genome AF: 0.245 AC: 37325AN: 152134Hom.: 4756 Cov.: 32 AF XY: 0.247 AC XY: 18368AN XY: 74372
ClinVar
Submissions by phenotype
not specified Benign:3
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not provided Benign:2
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Thrombophilia due to activated protein C resistance Benign:2
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Congenital factor V deficiency Benign:1
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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. -
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