10-99877145-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_015221.4(DNMBP):c.*6C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000299 in 1,600,032 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 (no stars).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00031 ( 0 hom. )
Consequence
DNMBP
NM_015221.4 3_prime_UTR
NM_015221.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.613
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 Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 10-99877145-G-A is Benign according to our data. Variant chr10-99877145-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3048708.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNMBP | NM_015221.4 | c.*6C>T | 3_prime_UTR_variant | 17/17 | ENST00000324109.9 | NP_056036.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNMBP | ENST00000324109.9 | c.*6C>T | 3_prime_UTR_variant | 17/17 | 1 | NM_015221.4 | ENSP00000315659 | P1 | ||
DNMBP | ENST00000543621.6 | c.*6C>T | 3_prime_UTR_variant | 14/14 | 1 | ENSP00000443657 | ||||
DNMBP | ENST00000636706.1 | c.*6C>T | 3_prime_UTR_variant | 14/14 | 2 | ENSP00000489875 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152102Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000161 AC: 38AN: 235718Hom.: 0 AF XY: 0.000157 AC XY: 20AN XY: 127566
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GnomAD4 exome AF: 0.000312 AC: 452AN: 1447930Hom.: 0 Cov.: 31 AF XY: 0.000283 AC XY: 204AN XY: 719608
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GnomAD4 genome AF: 0.000171 AC: 26AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74288
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
DNMBP-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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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