chr10-73766103-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_198597.3(SEC24C):c.1500C>A(p.Ser500Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000862 in 1,613,170 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 (no stars).
Frequency
Consequence
NM_198597.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC24C | NM_198597.3 | c.1500C>A | p.Ser500Arg | missense_variant | 11/23 | ENST00000345254.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC24C | ENST00000345254.9 | c.1500C>A | p.Ser500Arg | missense_variant | 11/23 | 1 | NM_198597.3 | P1 | |
SEC24C | ENST00000465076.5 | c.1500C>A | p.Ser500Arg | missense_variant, NMD_transcript_variant | 11/22 | 1 | |||
SEC24C | ENST00000339365.2 | c.1500C>A | p.Ser500Arg | missense_variant | 12/24 | 5 | P1 | ||
SEC24C | ENST00000635550.1 | c.*890C>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/23 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000192 AC: 48AN: 250594Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135518
GnomAD4 exome AF: 0.0000883 AC: 129AN: 1460902Hom.: 0 Cov.: 32 AF XY: 0.0000867 AC XY: 63AN XY: 726808
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74442
ClinVar
Submissions by phenotype
Microcephaly Uncertain:1
Uncertain significance, no assertion criteria provided | research | Department of Pediatrics, Samsung Medical Center, Samsung Medical Center | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at