chr10-99880039-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015221.4(DNMBP):c.4320C>T(p.Ser1440=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 1,613,852 control chromosomes in the GnomAD database, including 211,787 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.50 ( 19745 hom., cov: 32)
Exomes 𝑓: 0.51 ( 192042 hom. )
Consequence
DNMBP
NM_015221.4 synonymous
NM_015221.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.845
Genes affected
DNMBP (HGNC:30373): (dynamin binding protein) This gene encodes a protein belonging to the guanine nucleotide exchange factor family, and which regulates the configuration of cell junctions. It contains multiple binding sites for dynamin and thus links dynamin to actin regulatory proteins. Polymorphisms in this gene have been linked to Alzheimer's disease in some populations, though there are conflicting reports of such linkages in other populations. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 10-99880039-G-A is Benign according to our data. Variant chr10-99880039-G-A is described in ClinVar as [Benign]. Clinvar id is 1255519.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNMBP | NM_015221.4 | c.4320C>T | p.Ser1440= | synonymous_variant | 16/17 | ENST00000324109.9 | NP_056036.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNMBP | ENST00000324109.9 | c.4320C>T | p.Ser1440= | synonymous_variant | 16/17 | 1 | NM_015221.4 | ENSP00000315659 | P1 | |
DNMBP | ENST00000543621.6 | c.2184C>T | p.Ser728= | synonymous_variant | 13/14 | 1 | ENSP00000443657 | |||
DNMBP | ENST00000636706.1 | c.3216C>T | p.Ser1072= | synonymous_variant | 13/14 | 2 | ENSP00000489875 |
Frequencies
GnomAD3 genomes AF: 0.505 AC: 76657AN: 151900Hom.: 19712 Cov.: 32
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GnomAD3 exomes AF: 0.484 AC: 121671AN: 251458Hom.: 30185 AF XY: 0.487 AC XY: 66238AN XY: 135908
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GnomAD4 exome AF: 0.509 AC: 744586AN: 1461834Hom.: 192042 Cov.: 72 AF XY: 0.510 AC XY: 370684AN XY: 727218
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GnomAD4 genome AF: 0.505 AC: 76746AN: 152018Hom.: 19745 Cov.: 32 AF XY: 0.501 AC XY: 37216AN XY: 74294
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
DNMBP-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Cataract 48 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational 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