4-118723565-C-CTT
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_014822.4(SEC24D):c.3048_3049insAA(p.Val1017LysfsTer19) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,670 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. Y1016Y) has been classified as Likely benign.
Frequency
Consequence
NM_014822.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC24D | NM_014822.4 | c.3048_3049insAA | p.Val1017LysfsTer19 | frameshift_variant | 23/23 | ENST00000280551.11 | |
SEC24D | NM_001318066.2 | c.3051_3052insAA | p.Val1018LysfsTer19 | frameshift_variant | 23/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC24D | ENST00000280551.11 | c.3048_3049insAA | p.Val1017LysfsTer19 | frameshift_variant | 23/23 | 1 | NM_014822.4 | P1 | |
SEC24D | ENST00000511481.5 | c.1941_1942insAA | p.Val648LysfsTer19 | frameshift_variant | 16/16 | 1 | |||
SEC24D | ENST00000502830.1 | n.377_378insAA | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
SEC24D | ENST00000505134.5 | n.3179_3180insAA | non_coding_transcript_exon_variant | 18/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251046Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135680
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461658Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727122
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152012Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74234
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 14, 2023 | Frameshift variant predicted to result in protein elongation as the last 16 amino acids are replaced with 18 different amino acids, although loss-of-function variants have not been reported downstream of this position in the protein; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at