13-77591444-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144777.3(SCEL):c.676G>A(p.Ala226Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,573,556 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCEL | NM_144777.3 | c.676G>A | p.Ala226Thr | missense_variant | 11/33 | ENST00000349847.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCEL | ENST00000349847.4 | c.676G>A | p.Ala226Thr | missense_variant | 11/33 | 1 | NM_144777.3 | P2 | |
SCEL | ENST00000377246.7 | c.676G>A | p.Ala226Thr | missense_variant | 11/32 | 1 | A2 | ||
SCEL | ENST00000535157.5 | c.610G>A | p.Ala204Thr | missense_variant | 10/31 | 2 | A2 | ||
SCEL | ENST00000471491.5 | c.607G>A | p.Ala203Thr | missense_variant, NMD_transcript_variant | 10/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000566 AC: 14AN: 247276Hom.: 0 AF XY: 0.0000599 AC XY: 8AN XY: 133640
GnomAD4 exome AF: 0.0000253 AC: 36AN: 1421310Hom.: 0 Cov.: 25 AF XY: 0.0000352 AC XY: 25AN XY: 709384
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.676G>A (p.A226T) alteration is located in exon 11 (coding exon 10) of the SCEL gene. This alteration results from a G to A substitution at nucleotide position 676, causing the alanine (A) at amino acid position 226 to be replaced by a threonine (T). 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