1-197040649-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001994.3(F13B):c.1825G>A(p.Gly609Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 1,460,638 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001994.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F13B | ENST00000367412.2 | c.1825G>A | p.Gly609Ser | missense_variant | Exon 11 of 12 | 1 | NM_001994.3 | ENSP00000356382.2 | ||
F13B | ENST00000649282.1 | c.580G>A | p.Gly194Ser | missense_variant | Exon 4 of 5 | ENSP00000497116.1 | ||||
F13B | ENST00000490002.1 | n.236G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250796Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135594
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460638Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 726648
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1825G>A (p.G609S) alteration is located in exon 11 (coding exon 11) of the F13B gene. This alteration results from a G to A substitution at nucleotide position 1825, causing the glycine (G) at amino acid position 609 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at