5-134666915-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021982.3(SEC24A):c.658C>T(p.Pro220Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000617 in 1,459,170 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_021982.3 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 |
---|---|---|---|---|---|---|---|
SEC24A | NM_021982.3 | c.658C>T | p.Pro220Ser | missense_variant | 3/23 | ENST00000398844.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC24A | ENST00000398844.7 | c.658C>T | p.Pro220Ser | missense_variant | 3/23 | 2 | NM_021982.3 | P1 | |
SEC24A | ENST00000322887.8 | c.658C>T | p.Pro220Ser | missense_variant | 3/13 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249200Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135226
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1459170Hom.: 0 Cov.: 31 AF XY: 0.00000689 AC XY: 5AN XY: 726080
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2022 | The c.658C>T (p.P220S) alteration is located in exon 3 (coding exon 3) of the SEC24A gene. This alteration results from a C to T substitution at nucleotide position 658, causing the proline (P) at amino acid position 220 to be replaced by a serine (S). 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