3-10305108-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_183352.3(SEC13):c.633C>A(p.His211Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000558 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H211Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_183352.3 missense
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 |
---|---|---|---|---|---|---|---|
SEC13 | NM_183352.3 | c.633C>A | p.His211Gln | missense_variant | 7/9 | ENST00000350697.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC13 | ENST00000350697.8 | c.633C>A | p.His211Gln | missense_variant | 7/9 | 1 | NM_183352.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251058Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135660
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727202
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2023 | The c.633C>A (p.H211Q) alteration is located in exon 7 (coding exon 7) of the SEC13 gene. This alteration results from a C to A substitution at nucleotide position 633, causing the histidine (H) at amino acid position 211 to be replaced by a glutamine (Q). 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