chr18-63901869-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_002575.3(SERPINB2):āc.665T>Cā(p.Phe222Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000113 in 1,599,768 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 (ā ).
Frequency
Consequence
NM_002575.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SERPINB2 | NM_002575.3 | c.665T>C | p.Phe222Ser | missense_variant | Exon 6 of 8 | ENST00000299502.9 | NP_002566.1 | |
SERPINB2 | NM_001143818.2 | c.665T>C | p.Phe222Ser | missense_variant | Exon 7 of 9 | NP_001137290.1 | ||
SERPINB2 | XM_024451192.2 | c.665T>C | p.Phe222Ser | missense_variant | Exon 6 of 8 | XP_024306960.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERPINB2 | ENST00000299502.9 | c.665T>C | p.Phe222Ser | missense_variant | Exon 6 of 8 | 1 | NM_002575.3 | ENSP00000299502.4 | ||
ENSG00000289724 | ENST00000397996.6 | c.293T>C | p.Phe98Ser | missense_variant | Exon 3 of 8 | 5 | ENSP00000381082.2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000127 AC: 3AN: 236490Hom.: 0 AF XY: 0.00000780 AC XY: 1AN XY: 128192
GnomAD4 exome AF: 0.00000553 AC: 8AN: 1447564Hom.: 0 Cov.: 30 AF XY: 0.00000695 AC XY: 5AN XY: 719836
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.665T>C (p.F222S) alteration is located in exon 7 (coding exon 5) of the SERPINB2 gene. This alteration results from a T to C substitution at nucleotide position 665, causing the phenylalanine (F) at amino acid position 222 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