13-77556623-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144777.3(SCEL):āc.71C>Gā(p.Thr24Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,866 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 (ā ).
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.71C>G | p.Thr24Arg | missense_variant | 3/33 | ENST00000349847.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCEL | ENST00000349847.4 | c.71C>G | p.Thr24Arg | missense_variant | 3/33 | 1 | NM_144777.3 | P2 | |
SCEL | ENST00000377246.7 | c.71C>G | p.Thr24Arg | missense_variant | 3/32 | 1 | A2 | ||
SCEL | ENST00000535157.5 | c.71C>G | p.Thr24Arg | missense_variant | 3/31 | 2 | A2 | ||
SCEL | ENST00000471491.5 | c.71C>G | p.Thr24Arg | missense_variant, NMD_transcript_variant | 3/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251326Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135818
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461700Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727164
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 25, 2023 | The c.71C>G (p.T24R) alteration is located in exon 3 (coding exon 2) of the SCEL gene. This alteration results from a C to G substitution at nucleotide position 71, causing the threonine (T) at amino acid position 24 to be replaced by an arginine (R). 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