rs886041029
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_007214.5(SEC63):c.1703_1705delAAG(p.Glu568del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0025 in 1,612,242 control chromosomes in the GnomAD database, including 21 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_007214.5 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEC63 | NM_007214.5 | c.1703_1705delAAG | p.Glu568del | disruptive_inframe_deletion | Exon 17 of 21 | ENST00000369002.9 | NP_009145.1 | |
SEC63 | XM_047418130.1 | c.1535_1537delAAG | p.Glu512del | disruptive_inframe_deletion | Exon 17 of 21 | XP_047274086.1 | ||
SEC63 | XM_047418131.1 | c.1283_1285delAAG | p.Glu428del | disruptive_inframe_deletion | Exon 16 of 20 | XP_047274087.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEC63 | ENST00000369002.9 | c.1703_1705delAAG | p.Glu568del | disruptive_inframe_deletion | Exon 17 of 21 | 1 | NM_007214.5 | ENSP00000357998.4 | ||
SEC63 | ENST00000473746.1 | n.350_352delAAG | non_coding_transcript_exon_variant | Exon 1 of 4 | 2 | |||||
SEC63 | ENST00000465210.1 | n.-6_-4delAAG | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00261 AC: 397AN: 152144Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00369 AC: 926AN: 250706Hom.: 5 AF XY: 0.00356 AC XY: 483AN XY: 135556
GnomAD4 exome AF: 0.00249 AC: 3640AN: 1459980Hom.: 16 AF XY: 0.00244 AC XY: 1770AN XY: 726412
GnomAD4 genome AF: 0.00261 AC: 397AN: 152262Hom.: 5 Cov.: 32 AF XY: 0.00320 AC XY: 238AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:4
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See Variant Classification Assertion Criteria. -
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Polycystic liver disease 1 Uncertain:1Benign:1
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Polycystic liver disease 2 Pathogenic:1
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SEC63-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at