chr18-63589678-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001348267.2(SERPINB13):c.-214C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000249 in 1,613,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001348267.2 5_prime_UTR_premature_start_codon_gain
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 |
---|---|---|---|---|---|---|---|---|
SERPINB13 | NM_012397.4 | c.188C>T | p.Thr63Met | missense_variant | Exon 3 of 8 | ENST00000344731.10 | NP_036529.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000277 AC: 42AN: 151752Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000243 AC: 61AN: 250922Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135602
GnomAD4 exome AF: 0.000246 AC: 359AN: 1461360Hom.: 0 Cov.: 31 AF XY: 0.000215 AC XY: 156AN XY: 726964
GnomAD4 genome AF: 0.000277 AC: 42AN: 151868Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74186
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.188C>T (p.T63M) alteration is located in exon 3 (coding exon 2) of the SERPINB13 gene. This alteration results from a C to T substitution at nucleotide position 188, causing the threonine (T) at amino acid position 63 to be replaced by a methionine (M). 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