rs4282891
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000373241.9(SAR1A):c.-17+100T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 91,048 control chromosomes in the GnomAD database, including 29,435 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 0.82 ( 29435 hom., cov: 11)
Exomes 𝑓: 0.50 ( 0 hom. )
Consequence
SAR1A
ENST00000373241.9 intron
ENST00000373241.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.167
Genes affected
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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=-0.56).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAR1A | NM_020150.5 | c.-17+100T>G | intron_variant | ENST00000373241.9 | NP_064535.1 | |||
SAR1A | NM_001142648.2 | c.-87+100T>G | intron_variant | NP_001136120.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAR1A | ENST00000373241.9 | c.-17+100T>G | intron_variant | 1 | NM_020150.5 | ENSP00000362338 | P1 | |||
SAR1A | ENST00000373239.2 | c.-217+100T>G | intron_variant | 3 | ENSP00000362336 | |||||
SAR1A | ENST00000373242.6 | c.-87+100T>G | intron_variant | 2 | ENSP00000362339 | P1 |
Frequencies
GnomAD3 genomes AF: 0.823 AC: 74880AN: 91024Hom.: 29437 Cov.: 11
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GnomAD4 exome AF: 0.500 AC: 1AN: 2Hom.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome AF: 0.823 AC: 74891AN: 91046Hom.: 29435 Cov.: 11 AF XY: 0.818 AC XY: 34993AN XY: 42790
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at