10-99955546-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_015221.4(DNMBP):​c.1928G>A​(p.Arg643His) variant causes a missense change. The variant allele was found at a frequency of 0.0000357 in 1,598,388 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 Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000085 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000030 ( 0 hom. )

Consequence

DNMBP
NM_015221.4 missense

Scores

6
4
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.02
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]
DNMBP-AS1 (HGNC:20431): (DNMBP antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06461653).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DNMBPNM_015221.4 linkuse as main transcriptc.1928G>A p.Arg643His missense_variant 4/17 ENST00000324109.9 NP_056036.1
DNMBP-AS1NR_024130.3 linkuse as main transcriptn.177-128C>T intron_variant, non_coding_transcript_variant
DNMBPXM_011539559.3 linkuse as main transcriptc.1928G>A p.Arg643His missense_variant 5/18 XP_011537861.1
DNMBPXM_047424910.1 linkuse as main transcriptc.1928G>A p.Arg643His missense_variant 5/18 XP_047280866.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DNMBPENST00000324109.9 linkuse as main transcriptc.1928G>A p.Arg643His missense_variant 4/171 NM_015221.4 ENSP00000315659 P1Q6XZF7-1
DNMBP-AS1ENST00000661385.1 linkuse as main transcriptn.223-936C>T intron_variant, non_coding_transcript_variant
DNMBP-AS1ENST00000434409.2 linkuse as main transcriptn.173-128C>T intron_variant, non_coding_transcript_variant 2
DNMBP-AS1ENST00000661150.1 linkuse as main transcriptn.177-1243C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0000855
AC:
13
AN:
152110
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000524
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000965
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000159
AC:
38
AN:
238770
Hom.:
0
AF XY:
0.000163
AC XY:
21
AN XY:
129154
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000314
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00145
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000352
GnomAD4 exome
AF:
0.0000304
AC:
44
AN:
1446160
Hom.:
0
Cov.:
31
AF XY:
0.0000292
AC XY:
21
AN XY:
718136
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000263
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000657
Gnomad4 SAS exome
AF:
0.0000119
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000272
Gnomad4 OTH exome
AF:
0.0000504
GnomAD4 genome
AF:
0.0000854
AC:
13
AN:
152228
Hom.:
0
Cov.:
32
AF XY:
0.000107
AC XY:
8
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000523
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000967
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000121
ExAC
AF:
0.000115
AC:
14

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 23, 2023The c.1928G>A (p.R643H) alteration is located in exon 4 (coding exon 3) of the DNMBP gene. This alteration results from a G to A substitution at nucleotide position 1928, causing the arginine (R) at amino acid position 643 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.68
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.25
CADD
Pathogenic
28
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.17
T
Eigen
Pathogenic
0.69
Eigen_PC
Pathogenic
0.67
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.91
D
M_CAP
Benign
0.048
D
MetaRNN
Benign
0.065
T
MetaSVM
Benign
-0.79
T
MutationAssessor
Uncertain
2.9
M
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-2.2
N
REVEL
Benign
0.23
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.32
MutPred
0.16
Loss of methylation at R643 (P = 0.0469);
MVP
0.87
MPC
0.70
ClinPred
0.34
T
GERP RS
6.0
Varity_R
0.23
gMVP
0.55

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: rs544922058; hg19: chr10-101715303; COSMIC: COSV60628445; API