chr6-2836221-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_030666.4(SERPINB1):āc.454A>Gā(p.Met152Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000895 in 1,452,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_030666.4 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 |
---|---|---|---|---|---|---|---|
SERPINB1 | NM_030666.4 | c.454A>G | p.Met152Val | missense_variant | 5/7 | ENST00000380739.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINB1 | ENST00000380739.6 | c.454A>G | p.Met152Val | missense_variant | 5/7 | 1 | NM_030666.4 | P1 | |
SERPINB1 | ENST00000468511.5 | n.148A>G | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
SERPINB1 | ENST00000476896.5 | n.759A>G | non_coding_transcript_exon_variant | 6/6 | 5 | ||||
SERPINB1 | ENST00000490094.5 | n.501A>G | non_coding_transcript_exon_variant | 5/6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000895 AC: 13AN: 1452884Hom.: 0 Cov.: 34 AF XY: 0.0000111 AC XY: 8AN XY: 722152
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2023 | 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