10-99955252-T-C

Variant summary

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

The NM_015221.4(DNMBP):ā€‹c.2222A>Gā€‹(p.Asn741Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000273 in 1,613,904 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.00011 ( 0 hom., cov: 32)
Exomes š‘“: 0.00029 ( 0 hom. )

Consequence

DNMBP
NM_015221.4 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.85
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=0.05495581).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DNMBPNM_015221.4 linkuse as main transcriptc.2222A>G p.Asn741Ser missense_variant 4/17 ENST00000324109.9 NP_056036.1
DNMBP-AS1NR_024130.3 linkuse as main transcriptn.177-422T>C intron_variant, non_coding_transcript_variant
DNMBPXM_011539559.3 linkuse as main transcriptc.2222A>G p.Asn741Ser missense_variant 5/18 XP_011537861.1
DNMBPXM_047424910.1 linkuse as main transcriptc.2222A>G p.Asn741Ser 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.2222A>G p.Asn741Ser missense_variant 4/171 NM_015221.4 ENSP00000315659 P1Q6XZF7-1
DNMBP-AS1ENST00000661385.1 linkuse as main transcriptn.223-1230T>C intron_variant, non_coding_transcript_variant
DNMBP-AS1ENST00000434409.2 linkuse as main transcriptn.173-422T>C intron_variant, non_coding_transcript_variant 2
DNMBP-AS1ENST00000661150.1 linkuse as main transcriptn.177-1537T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.000105
AC:
16
AN:
152190
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000206
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000167
AC:
42
AN:
250988
Hom.:
0
AF XY:
0.000155
AC XY:
21
AN XY:
135638
show subpopulations
Gnomad AFR exome
AF:
0.000123
Gnomad AMR exome
AF:
0.000434
Gnomad ASJ exome
AF:
0.000198
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000194
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.000291
AC:
425
AN:
1461714
Hom.:
0
Cov.:
31
AF XY:
0.000271
AC XY:
197
AN XY:
727134
show subpopulations
Gnomad4 AFR exome
AF:
0.0000896
Gnomad4 AMR exome
AF:
0.000291
Gnomad4 ASJ exome
AF:
0.000191
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000352
Gnomad4 OTH exome
AF:
0.000199
GnomAD4 genome
AF:
0.000105
AC:
16
AN:
152190
Hom.:
0
Cov.:
32
AF XY:
0.0000404
AC XY:
3
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000206
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000227
Hom.:
0
Bravo
AF:
0.000147
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000778
AC:
3
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000349
AC:
3
ExAC
AF:
0.000189
AC:
23
EpiCase
AF:
0.000436
EpiControl
AF:
0.000296

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 GeneticsFeb 09, 2022The c.2222A>G (p.N741S) alteration is located in exon 4 (coding exon 3) of the DNMBP gene. This alteration results from a A to G substitution at nucleotide position 2222, causing the asparagine (N) at amino acid position 741 to be replaced by a serine (S). 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
0.071
BayesDel_addAF
Benign
-0.58
T
BayesDel_noAF
Benign
-0.75
CADD
Benign
16
DANN
Uncertain
0.98
DEOGEN2
Benign
0.032
T
Eigen
Benign
-0.41
Eigen_PC
Benign
-0.28
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Benign
0.76
T
M_CAP
Benign
0.0099
T
MetaRNN
Benign
0.055
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.9
L
MutationTaster
Benign
0.98
N;N
PrimateAI
Benign
0.31
T
PROVEAN
Benign
-1.2
N
REVEL
Benign
0.077
Sift
Benign
0.20
T
Sift4G
Benign
0.13
T
Polyphen
0.027
B
Vest4
0.060
MVP
0.56
MPC
0.12
ClinPred
0.031
T
GERP RS
3.5
Varity_R
0.045
gMVP
0.11

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: rs137876820; hg19: chr10-101715009; API