chr13-77563871-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144777.3(SCEL):c.262C>T(p.Arg88Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000213 in 1,597,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144777.3 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCEL | NM_144777.3 | c.262C>T | p.Arg88Trp | missense_variant | 5/33 | ENST00000349847.4 | NP_659001.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCEL | ENST00000349847.4 | c.262C>T | p.Arg88Trp | missense_variant | 5/33 | 1 | NM_144777.3 | ENSP00000302579 | P2 | |
SCEL | ENST00000377246.7 | c.262C>T | p.Arg88Trp | missense_variant | 5/32 | 1 | ENSP00000366454 | A2 | ||
SCEL | ENST00000535157.5 | c.262C>T | p.Arg88Trp | missense_variant | 5/31 | 2 | ENSP00000437895 | A2 | ||
SCEL | ENST00000471491.5 | c.262C>T | p.Arg88Trp | missense_variant, NMD_transcript_variant | 5/19 | 2 | ENSP00000432840 |
Frequencies
GnomAD3 genomes AF: 0.0000331 AC: 5AN: 150842Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000336 AC: 8AN: 237788Hom.: 0 AF XY: 0.0000545 AC XY: 7AN XY: 128524
GnomAD4 exome AF: 0.0000200 AC: 29AN: 1446942Hom.: 0 Cov.: 30 AF XY: 0.0000250 AC XY: 18AN XY: 719182
GnomAD4 genome AF: 0.0000331 AC: 5AN: 150842Hom.: 0 Cov.: 32 AF XY: 0.0000680 AC XY: 5AN XY: 73508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.262C>T (p.R88W) alteration is located in exon 5 (coding exon 4) of the SCEL gene. This alteration results from a C to T substitution at nucleotide position 262, causing the arginine (R) at amino acid position 88 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