13-77602704-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144777.3(SCEL):c.1028C>T(p.Thr343Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000837 in 1,613,354 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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.1028C>T | p.Thr343Met | missense_variant | 17/33 | ENST00000349847.4 | |
SCEL-AS1 | NR_126413.1 | n.76-454G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCEL | ENST00000349847.4 | c.1028C>T | p.Thr343Met | missense_variant | 17/33 | 1 | NM_144777.3 | P2 | |
SCEL-AS1 | ENST00000457528.6 | n.76-454G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000108 AC: 27AN: 251004Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135634
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1461136Hom.: 0 Cov.: 29 AF XY: 0.0000880 AC XY: 64AN XY: 726874
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.1028C>T (p.T343M) alteration is located in exon 17 (coding exon 16) of the SCEL gene. This alteration results from a C to T substitution at nucleotide position 1028, causing the threonine (T) at amino acid position 343 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