rs2038479
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000627582.3(DNM3):c.236-17506C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 509,006 control chromosomes in the GnomAD database, including 153,316 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 0.81 ( 49510 hom., cov: 31)
Exomes 𝑓: 0.76 ( 103806 hom. )
Consequence
DNM3
ENST00000627582.3 intron
ENST00000627582.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.594
Genes affected
DNM3 (HGNC:29125): (dynamin 3) This gene encodes a member of a family of guanosine triphosphate (GTP)-binding proteins that associate with microtubules and are involved in vesicular transport. The encoded protein functions in the development of megakaryocytes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]
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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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNM3 | NM_015569.5 | c.236-17506C>A | intron_variant | ENST00000627582.3 | NP_056384.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNM3 | ENST00000627582.3 | c.236-17506C>A | intron_variant | 1 | NM_015569.5 | ENSP00000486701 | A1 |
Frequencies
GnomAD3 genomes AF: 0.807 AC: 122607AN: 151954Hom.: 49462 Cov.: 31
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GnomAD4 exome AF: 0.762 AC: 271864AN: 356938Hom.: 103806 Cov.: 2 AF XY: 0.764 AC XY: 128658AN XY: 168506
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GnomAD4 genome AF: 0.807 AC: 122714AN: 152068Hom.: 49510 Cov.: 31 AF XY: 0.805 AC XY: 59789AN XY: 74308
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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