chr18-63564119-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001307928.2(SERPINB12):c.704C>T(p.Ala235Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000521 in 1,611,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/25 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001307928.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINB12 | NM_001307928.2 | c.704C>T | p.Ala235Val | missense_variant, splice_region_variant | 6/8 | ENST00000382768.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINB12 | ENST00000382768.2 | c.704C>T | p.Ala235Val | missense_variant, splice_region_variant | 6/8 | 1 | NM_001307928.2 | P1 | |
SERPINB12 | ENST00000269491.6 | c.644C>T | p.Ala215Val | missense_variant, splice_region_variant | 6/8 | 1 | |||
SERPINB12 | ENST00000680447.1 | n.441C>T | splice_region_variant, non_coding_transcript_exon_variant | 2/4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000323 AC: 8AN: 248002Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133882
GnomAD4 exome AF: 0.0000562 AC: 82AN: 1459018Hom.: 0 Cov.: 32 AF XY: 0.0000593 AC XY: 43AN XY: 725642
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.644C>T (p.A215V) alteration is located in exon 5 (coding exon 5) of the SERPINB12 gene. This alteration results from a C to T substitution at nucleotide position 644, causing the alanine (A) at amino acid position 215 to be replaced by a valine (V). 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