13-77617648-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144777.3(SCEL):c.1501A>C(p.Asn501His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 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 | UniProt |
---|---|---|---|---|---|---|---|
SCEL | NM_144777.3 | c.1501A>C | p.Asn501His | missense_variant | 25/33 | ENST00000349847.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCEL | ENST00000349847.4 | c.1501A>C | p.Asn501His | missense_variant | 25/33 | 1 | NM_144777.3 | P2 | |
SCEL | ENST00000377246.7 | c.1441A>C | p.Asn481His | missense_variant | 24/32 | 1 | A2 | ||
SCEL | ENST00000535157.5 | c.1375A>C | p.Asn459His | missense_variant | 23/31 | 2 | A2 | ||
SCEL | ENST00000469982.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 28
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2022 | The c.1501A>C (p.N501H) alteration is located in exon 25 (coding exon 24) of the SCEL gene. This alteration results from a A to C substitution at nucleotide position 1501, causing the asparagine (N) at amino acid position 501 to be replaced by a histidine (H). 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
Publications
No publications associated with this variant yet.