18-63895339-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002575.3(SERPINB2):c.244A>T(p.Met82Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000836 in 1,614,186 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 Uncertain significance (★).
Frequency
Consequence
NM_002575.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SERPINB2 | NM_002575.3 | c.244A>T | p.Met82Leu | missense_variant | Exon 3 of 8 | ENST00000299502.9 | NP_002566.1 | |
SERPINB2 | NM_001143818.2 | c.244A>T | p.Met82Leu | missense_variant | Exon 4 of 9 | NP_001137290.1 | ||
SERPINB2 | XM_024451192.2 | c.244A>T | p.Met82Leu | missense_variant | Exon 3 of 8 | XP_024306960.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000147 AC: 37AN: 251394Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135860
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.0000798 AC XY: 58AN XY: 727214
GnomAD4 genome AF: 0.000131 AC: 20AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.244A>T (p.M82L) alteration is located in exon 4 (coding exon 2) of the SERPINB2 gene. This alteration results from a A to T substitution at nucleotide position 244, causing the methionine (M) at amino acid position 82 to be replaced by a leucine (L). 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