9-128237193-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000372923.8(DNM1):​c.1423-2252G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,936 control chromosomes in the GnomAD database, including 14,411 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 14411 hom., cov: 32)

Consequence

DNM1
ENST00000372923.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.884
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DNM1NM_004408.4 linkuse as main transcriptc.1423-2252G>C intron_variant ENST00000372923.8 NP_004399.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DNM1ENST00000372923.8 linkuse as main transcriptc.1423-2252G>C intron_variant 1 NM_004408.4 ENSP00000362014 A1Q05193-1

Frequencies

GnomAD3 genomes
AF:
0.376
AC:
57034
AN:
151818
Hom.:
14355
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.716
Gnomad AMI
AF:
0.132
Gnomad AMR
AF:
0.273
Gnomad ASJ
AF:
0.288
Gnomad EAS
AF:
0.494
Gnomad SAS
AF:
0.401
Gnomad FIN
AF:
0.233
Gnomad MID
AF:
0.335
Gnomad NFE
AF:
0.212
Gnomad OTH
AF:
0.355
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.376
AC:
57152
AN:
151936
Hom.:
14411
Cov.:
32
AF XY:
0.377
AC XY:
28010
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.717
Gnomad4 AMR
AF:
0.273
Gnomad4 ASJ
AF:
0.288
Gnomad4 EAS
AF:
0.494
Gnomad4 SAS
AF:
0.402
Gnomad4 FIN
AF:
0.233
Gnomad4 NFE
AF:
0.212
Gnomad4 OTH
AF:
0.358
Alfa
AF:
0.127
Hom.:
211
Bravo
AF:
0.392
Asia WGS
AF:
0.460
AC:
1597
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.72
DANN
Benign
0.43

Splicing

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: rs7022174; hg19: chr9-130999472; API