rs198426
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000257215.10(DAGLA):c.409+54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 1,378,648 control chromosomes in the GnomAD database, including 67,289 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 0.24 ( 5456 hom., cov: 33)
Exomes 𝑓: 0.30 ( 61833 hom. )
Consequence
DAGLA
ENST00000257215.10 intron
ENST00000257215.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.358
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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DAGLA | NM_006133.3 | c.409+54C>T | intron_variant | ENST00000257215.10 | NP_006124.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DAGLA | ENST00000257215.10 | c.409+54C>T | intron_variant | 1 | NM_006133.3 | ENSP00000257215 | P1 | |||
DAGLA | ENST00000540717.1 | c.386+54C>T | intron_variant, NMD_transcript_variant | 5 | ENSP00000440264 |
Frequencies
GnomAD3 genomes AF: 0.235 AC: 35792AN: 152066Hom.: 5456 Cov.: 33
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GnomAD4 exome AF: 0.304 AC: 373292AN: 1226466Hom.: 61833 AF XY: 0.303 AC XY: 188263AN XY: 622010
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GnomAD4 genome AF: 0.235 AC: 35783AN: 152182Hom.: 5456 Cov.: 33 AF XY: 0.233 AC XY: 17329AN XY: 74402
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ClinVar
Not reported inComputational scores
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Name
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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