10-73760299-C-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_198597.3(SEC24C):āc.763C>Gā(p.Pro255Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000775 in 1,613,514 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_198597.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEC24C | NM_198597.3 | c.763C>G | p.Pro255Ala | missense_variant | 5/23 | ENST00000345254.9 | NP_940999.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEC24C | ENST00000345254.9 | c.763C>G | p.Pro255Ala | missense_variant | 5/23 | 1 | NM_198597.3 | ENSP00000321845.6 |
Frequencies
GnomAD3 genomes AF: 0.00424 AC: 645AN: 152186Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00104 AC: 261AN: 250678Hom.: 1 AF XY: 0.000797 AC XY: 108AN XY: 135562
GnomAD4 exome AF: 0.000415 AC: 606AN: 1461210Hom.: 2 Cov.: 32 AF XY: 0.000373 AC XY: 271AN XY: 726966
GnomAD4 genome AF: 0.00423 AC: 644AN: 152304Hom.: 3 Cov.: 32 AF XY: 0.00400 AC XY: 298AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 04, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at