rs246341
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021982.3(SEC24A):c.2266+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 1,572,916 control chromosomes in the GnomAD database, including 739,538 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.98 ( 72844 hom., cov: 29)
Exomes 𝑓: 0.97 ( 666694 hom. )
Consequence
SEC24A
NM_021982.3 intron
NM_021982.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.403
Genes affected
SEC24A (HGNC:10703): (SEC24 homolog A, COPII coat complex component) The protein encoded by this gene belongs to a family of proteins that are homologous to yeast Sec24. This protein is a component of coat protein II (COPII)-coated vesicles that mediate protein transport from the endoplasmic reticulum. COPII acts in the cytoplasm to promote the transport of secretory, plasma membrane, and vacuolar proteins from the endoplasmic reticulum to the golgi complex. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEC24A | NM_021982.3 | c.2266+30G>A | intron_variant | ENST00000398844.7 | NP_068817.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEC24A | ENST00000398844.7 | c.2266+30G>A | intron_variant | 2 | NM_021982.3 | ENSP00000381823 | P1 |
Frequencies
GnomAD3 genomes AF: 0.978 AC: 148730AN: 152030Hom.: 72781 Cov.: 29
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GnomAD3 exomes AF: 0.977 AC: 220095AN: 225330Hom.: 107518 AF XY: 0.976 AC XY: 119454AN XY: 122420
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GnomAD4 exome AF: 0.969 AC: 1376251AN: 1420768Hom.: 666694 Cov.: 23 AF XY: 0.969 AC XY: 685581AN XY: 707524
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GnomAD4 genome AF: 0.978 AC: 148852AN: 152148Hom.: 72844 Cov.: 29 AF XY: 0.979 AC XY: 72803AN XY: 74376
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at