chr10-99955591-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_015221.4(DNMBP):​c.1883A>T​(p.Asp628Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,460,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

DNMBP
NM_015221.4 missense

Scores

4
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.505
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)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08146843).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DNMBPNM_015221.4 linkuse as main transcriptc.1883A>T p.Asp628Val missense_variant 4/17 ENST00000324109.9 NP_056036.1
DNMBP-AS1NR_024130.3 linkuse as main transcriptn.177-83T>A intron_variant, non_coding_transcript_variant
DNMBPXM_011539559.3 linkuse as main transcriptc.1883A>T p.Asp628Val missense_variant 5/18 XP_011537861.1
DNMBPXM_047424910.1 linkuse as main transcriptc.1883A>T p.Asp628Val 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.1883A>T p.Asp628Val missense_variant 4/171 NM_015221.4 ENSP00000315659 P1Q6XZF7-1
DNMBP-AS1ENST00000661385.1 linkuse as main transcriptn.223-891T>A intron_variant, non_coding_transcript_variant
DNMBP-AS1ENST00000434409.2 linkuse as main transcriptn.173-83T>A intron_variant, non_coding_transcript_variant 2
DNMBP-AS1ENST00000661150.1 linkuse as main transcriptn.177-1198T>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000279
AC:
7
AN:
250794
Hom.:
0
AF XY:
0.0000443
AC XY:
6
AN XY:
135520
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000381
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1460964
Hom.:
0
Cov.:
31
AF XY:
0.00000550
AC XY:
4
AN XY:
726648
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.0000189
ExAC
AF:
0.0000247
AC:
3

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 GeneticsSep 13, 2023The c.1883A>T (p.D628V) alteration is located in exon 4 (coding exon 3) of the DNMBP gene. This alteration results from a A to T substitution at nucleotide position 1883, causing the aspartic acid (D) at amino acid position 628 to be replaced by a valine (V). 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
Benign
0.12
BayesDel_addAF
Benign
-0.37
T
BayesDel_noAF
Benign
-0.45
CADD
Benign
19
DANN
Uncertain
0.98
DEOGEN2
Benign
0.052
T
Eigen
Benign
-0.44
Eigen_PC
Benign
-0.38
FATHMM_MKL
Benign
0.65
D
LIST_S2
Benign
0.80
T
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.081
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.3
M
MutationTaster
Benign
0.84
D;D
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-1.7
N
REVEL
Benign
0.058
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.015
D
Polyphen
0.048
B
Vest4
0.39
MutPred
0.24
Loss of solvent accessibility (P = 0.0169);
MVP
0.63
MPC
0.23
ClinPred
0.12
T
GERP RS
2.4
Varity_R
0.16
gMVP
0.26

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: rs764452068; hg19: chr10-101715348; API