chr7-93889142-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006528.4(TFPI2):āc.353G>Cā(p.Ser118Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,613,392 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006528.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFPI2 | NM_006528.4 | c.353G>C | p.Ser118Thr | missense_variant | 3/5 | ENST00000222543.11 | |
TFPI2 | NM_001271003.2 | c.320G>C | p.Ser107Thr | missense_variant | 3/5 | ||
TFPI2 | NM_001271004.2 | c.353G>C | p.Ser118Thr | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFPI2 | ENST00000222543.11 | c.353G>C | p.Ser118Thr | missense_variant | 3/5 | 1 | NM_006528.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250338Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135360
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461230Hom.: 0 Cov.: 31 AF XY: 0.0000495 AC XY: 36AN XY: 726888
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.353G>C (p.S118T) alteration is located in exon 3 (coding exon 3) of the TFPI2 gene. This alteration results from a G to C substitution at nucleotide position 353, causing the serine (S) at amino acid position 118 to be replaced by a threonine (T). 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