rs566718787
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_004408.4(DNM1):c.2322G>T(p.Ser774=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,460,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000023 ( 0 hom. )
Consequence
DNM1
NM_004408.4 synonymous
NM_004408.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.23
Genes affected
DNM1 (HGNC:2972): (dynamin 1) This gene encodes a member of the dynamin subfamily of GTP-binding proteins. The encoded protein possesses unique mechanochemical properties used to tubulate and sever membranes, and is involved in clathrin-mediated endocytosis and other vesicular trafficking processes. Actin and other cytoskeletal proteins act as binding partners for the encoded protein, which can also self-assemble leading to stimulation of GTPase activity. More than sixty highly conserved copies of the 3' region of this gene are found elsewhere in the genome, particularly on chromosomes Y and 15. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 9-128250728-G-T is Benign according to our data. Variant chr9-128250728-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 542680.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.23 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNM1 | NM_004408.4 | c.2322G>T | p.Ser774= | synonymous_variant | 21/22 | ENST00000372923.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNM1 | ENST00000372923.8 | c.2322G>T | p.Ser774= | synonymous_variant | 21/22 | 1 | NM_004408.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151846Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000144 AC: 1AN: 69276Hom.: 0 AF XY: 0.0000251 AC XY: 1AN XY: 39850
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GnomAD4 exome AF: 0.00000229 AC: 3AN: 1308600Hom.: 0 Cov.: 31 AF XY: 0.00000155 AC XY: 1AN XY: 645190
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GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151954Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74254
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Developmental and epileptic encephalopathy, 31 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 27, 2023 | - - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at