10-99879911-T-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_015221.4(DNMBP):ā€‹c.4448A>Gā€‹(p.Asn1483Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000317 in 1,614,230 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: š‘“ 0.00018 ( 0 hom., cov: 32)
Exomes š‘“: 0.00033 ( 3 hom. )

Consequence

DNMBP
NM_015221.4 missense

Scores

1
18

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.537
Variant links:
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 -9 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0057646036).
BP6
Variant 10-99879911-T-C is Benign according to our data. Variant chr10-99879911-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3043207.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DNMBPNM_015221.4 linkuse as main transcriptc.4448A>G p.Asn1483Ser missense_variant 16/17 ENST00000324109.9 NP_056036.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DNMBPENST00000324109.9 linkuse as main transcriptc.4448A>G p.Asn1483Ser missense_variant 16/171 NM_015221.4 ENSP00000315659 P1Q6XZF7-1
DNMBPENST00000543621.6 linkuse as main transcriptc.2312A>G p.Asn771Ser missense_variant 13/141 ENSP00000443657
DNMBPENST00000636706.1 linkuse as main transcriptc.3344A>G p.Asn1115Ser missense_variant 13/142 ENSP00000489875

Frequencies

GnomAD3 genomes
AF:
0.000184
AC:
28
AN:
152218
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00538
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000640
AC:
161
AN:
251466
Hom.:
0
AF XY:
0.000817
AC XY:
111
AN XY:
135908
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00519
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000176
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000331
AC:
484
AN:
1461894
Hom.:
3
Cov.:
31
AF XY:
0.000466
AC XY:
339
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.0000597
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00518
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000809
Gnomad4 OTH exome
AF:
0.000348
GnomAD4 genome
AF:
0.000184
AC:
28
AN:
152336
Hom.:
0
Cov.:
32
AF XY:
0.000268
AC XY:
20
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00539
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000680
Hom.:
0
Bravo
AF:
0.0000378
ExAC
AF:
0.000700
AC:
85
Asia WGS
AF:
0.00289
AC:
10
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

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 providedclinical testingPreventionGenetics, part of Exact SciencesJun 25, 2019This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.080
BayesDel_addAF
Benign
-0.67
T
BayesDel_noAF
Benign
-0.74
CADD
Benign
10
DANN
Uncertain
0.99
DEOGEN2
Benign
0.028
.;.;T
Eigen
Benign
-0.69
Eigen_PC
Benign
-0.59
FATHMM_MKL
Benign
0.39
N
LIST_S2
Benign
0.81
T;T;T
M_CAP
Benign
0.0064
T
MetaRNN
Benign
0.0058
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
2.0
.;.;M
MutationTaster
Benign
0.98
N;N;N;N
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-1.5
.;.;N
REVEL
Benign
0.041
Sift
Benign
0.099
.;.;T
Sift4G
Benign
0.29
.;.;T
Polyphen
0.0080
.;.;B
Vest4
0.10
MVP
0.43
MPC
0.12
ClinPred
0.025
T
GERP RS
3.1
Varity_R
0.093
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200530625; hg19: chr10-101639668; API