rs769121301

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_004408.4(DNM1):c.1893+9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000201 in 1,595,990 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 (★★).

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000019 ( 0 hom. )

Consequence

DNM1
NM_004408.4 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.373

Publications

0 publications found

Variant links:

Genes affected

DNM1 (HGNC:2972): (dynamin 1) This gene encodes a member of the dynamin subfamily of GTP-binding proteins. The encoded protein possesses unique mechanochemical properties used to tubulate and sever membranes, and is involved in clathrin-mediated endocytosis and other vesicular trafficking processes. Actin and other cytoskeletal proteins act as binding partners for the encoded protein, which can also self-assemble leading to stimulation of GTPase activity. More than sixty highly conserved copies of the 3' region of this gene are found elsewhere in the genome, particularly on chromosomes Y and 15. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

DNM1 Gene-Disease associations (from GenCC):

genetic developmental and epileptic encephalopathy
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
developmental and epileptic encephalopathy, 31A
Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
developmental and epileptic encephalopathy, 31B
Inheritance: AR, AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
Lennox-Gastaut syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
undetermined early-onset epileptic encephalopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

DNM1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 9-128247495-C-A is Benign according to our data. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128247495-C-A is described in CliVar as Likely_benign. Clinvar id is 508423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNM1	NM_004408.4 link	c.1893+9C>A		intron_variant	Intron 17 of 21	ENST00000372923.8	NP_004399.2	Q05193-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNM1	ENST00000372923.8 link	c.1893+9C>A		intron_variant	Intron 17 of 21	1	NM_004408.4	ENSP00000362014.4		Q05193-1
DNM1	ENST00000634267.2 link	c.1893+9C>A		intron_variant	Intron 17 of 21	5		ENSP00000489096.1		A0A0U1RQP1

Frequencies

GnomAD3 genomes

AF:

0.0000263

AC:

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000206

AC:

AN:

242754

AF XY:

0.0000228

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 FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000456

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000194

AC:

AN:

1443846

Hom.:

Cov.:

AF XY:

0.0000209

AC XY:

AN XY:

716580

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33186

American (AMR)

AF:

0.00

AC:

AN:

43948

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25930

East Asian (EAS)

AF:

0.00

AC:

AN:

39272

South Asian (SAS)

AF:

0.00

AC:

AN:

85304

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53098

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5720

European-Non Finnish (NFE)

AF:

0.0000219

AC:

AN:

1097790

Other (OTH)

AF:

0.0000671

AC:

AN:

59598

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000263

AC:

AN:

152144

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41428

American (AMR)

AF:

0.0000654

AC:

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5198

South Asian (SAS)

AF:

0.00

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

314

European-Non Finnish (NFE)

AF:

0.0000441

AC:

AN:

68020

Other (OTH)

AF:

0.00

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000658

Hom.:

Bravo

AF:

0.0000264

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 31A

Benign:1

Dec 24, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Mar 29, 2017

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Aug 14, 2018

Athena Diagnostics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

-0.37

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over