NM_002575.3:c.704T>A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_002575.3(SERPINB2):c.704T>A(p.Met235Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000639 in 1,613,028 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 (★).
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.704T>A | p.Met235Lys | missense_variant | Exon 7 of 8 | ENST00000299502.9 | NP_002566.1 | |
SERPINB2 | NM_001143818.2 | c.704T>A | p.Met235Lys | missense_variant | Exon 8 of 9 | NP_001137290.1 | ||
SERPINB2 | XM_024451192.2 | c.704T>A | p.Met235Lys | missense_variant | Exon 7 of 8 | XP_024306960.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERPINB2 | ENST00000299502.9 | c.704T>A | p.Met235Lys | missense_variant | Exon 7 of 8 | 1 | NM_002575.3 | ENSP00000299502.4 | ||
ENSG00000289724 | ENST00000397996.6 | c.332T>A | p.Met111Lys | missense_variant | Exon 4 of 8 | 5 | ENSP00000381082.2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000879 AC: 22AN: 250398Hom.: 0 AF XY: 0.0000812 AC XY: 11AN XY: 135406
GnomAD4 exome AF: 0.0000630 AC: 92AN: 1460862Hom.: 0 Cov.: 31 AF XY: 0.0000509 AC XY: 37AN XY: 726736
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.704T>A (p.M235K) alteration is located in exon 8 (coding exon 6) of the SERPINB2 gene. This alteration results from a T to A substitution at nucleotide position 704, causing the methionine (M) at amino acid position 235 to be replaced by a lysine (K). 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