rs2066870
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_021870.3(FGG):āc.418T>Cā(p.Tyr140His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 1,584,110 control chromosomes in the GnomAD database, including 137 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_021870.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGG | NM_021870.3 | c.418T>C | p.Tyr140His | missense_variant | 5/9 | ENST00000336098.8 | |
FGG | NM_000509.6 | c.418T>C | p.Tyr140His | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGG | ENST00000336098.8 | c.418T>C | p.Tyr140His | missense_variant | 5/9 | 2 | NM_021870.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0173 AC: 2632AN: 152146Hom.: 79 Cov.: 32
GnomAD3 exomes AF: 0.00474 AC: 1189AN: 250840Hom.: 27 AF XY: 0.00341 AC XY: 462AN XY: 135592
GnomAD4 exome AF: 0.00187 AC: 2680AN: 1431846Hom.: 58 Cov.: 28 AF XY: 0.00162 AC XY: 1160AN XY: 714272
GnomAD4 genome ? AF: 0.0173 AC: 2631AN: 152264Hom.: 79 Cov.: 32 AF XY: 0.0165 AC XY: 1228AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2021 | This variant is associated with the following publications: (PMID: 27884173, 19420351, 23467727) - |
Congenital afibrinogenemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | 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