18-63903295-C-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002575.3(SERPINB2):c.1238C>G(p.Ser413Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 1,526,154 control chromosomes in the GnomAD database, including 47,860 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002575.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINB2 | NM_002575.3 | c.1238C>G | p.Ser413Cys | missense_variant | 8/8 | ENST00000299502.9 | |
SERPINB2 | NM_001143818.2 | c.1238C>G | p.Ser413Cys | missense_variant | 9/9 | ||
SERPINB2 | XM_024451192.2 | c.1238C>G | p.Ser413Cys | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINB2 | ENST00000299502.9 | c.1238C>G | p.Ser413Cys | missense_variant | 8/8 | 1 | NM_002575.3 | P1 | |
SERPINB2 | ENST00000457692.5 | c.1238C>G | p.Ser413Cys | missense_variant | 9/9 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.286 AC: 43471AN: 151878Hom.: 6811 Cov.: 32
GnomAD3 exomes AF: 0.289 AC: 53535AN: 185116Hom.: 8685 AF XY: 0.282 AC XY: 27572AN XY: 97716
GnomAD4 exome AF: 0.237 AC: 326206AN: 1374158Hom.: 41028 Cov.: 32 AF XY: 0.238 AC XY: 160668AN XY: 674504
GnomAD4 genome ? AF: 0.286 AC: 43527AN: 151996Hom.: 6832 Cov.: 32 AF XY: 0.289 AC XY: 21504AN XY: 74282
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at