13-77572188-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_144777.3(SCEL):c.544C>T(p.Arg182Trp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000572 in 1,609,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144777.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCEL | NM_144777.3 | c.544C>T | p.Arg182Trp | missense_variant, splice_region_variant | 9/33 | ENST00000349847.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCEL | ENST00000349847.4 | c.544C>T | p.Arg182Trp | missense_variant, splice_region_variant | 9/33 | 1 | NM_144777.3 | P2 | |
ENST00000654937.1 | n.317-2238G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000600 AC: 15AN: 249932Hom.: 0 AF XY: 0.0000667 AC XY: 9AN XY: 135024
GnomAD4 exome AF: 0.0000576 AC: 84AN: 1457176Hom.: 0 Cov.: 30 AF XY: 0.0000662 AC XY: 48AN XY: 725000
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2022 | The c.544C>T (p.R182W) alteration is located in exon 9 (coding exon 8) of the SCEL gene. This alteration results from a C to T substitution at nucleotide position 544, causing the arginine (R) at amino acid position 182 to be replaced by a tryptophan (W). 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