18-63657373-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006919.3(SERPINB3):c.509G>A(p.Ser170Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000435 in 1,609,614 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 Likely benign (★).
Frequency
Consequence
NM_006919.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINB3 | NM_006919.3 | c.509G>A | p.Ser170Asn | missense_variant | 6/8 | ENST00000283752.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINB3 | ENST00000283752.10 | c.509G>A | p.Ser170Asn | missense_variant | 6/8 | 1 | NM_006919.3 | P1 | |
SERPINB3 | ENST00000332821.8 | c.509G>A | p.Ser170Asn | missense_variant | 6/7 | 1 | |||
SERPINB11 | ENST00000489748.5 | c.-16+1397C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249638Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134850
GnomAD4 exome AF: 0.0000254 AC: 37AN: 1457426Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 724902
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74336
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at