GeneBe

NM_001135556.2:c.314+54_314+56delAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001135556.2(DYNC1I1):​c.314+54_314+56delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,267,224 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000043 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

DYNC1I1
NM_001135556.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.299

Publications

0 publications found
Variant links:
Genes affected
DYNC1I1 (HGNC:2963): (dynein cytoplasmic 1 intermediate chain 1) Enables spectrin binding activity. Involved in vesicle transport along microtubule. Located in several cellular components, including kinetochore; recycling endosome; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135556.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DYNC1I1
NM_001135556.2
MANE Select
c.314+54_314+56delAAA
intron
N/ANP_001129028.1O14576-2
DYNC1I1
NM_004411.5
c.365+54_365+56delAAA
intron
N/ANP_004402.1O14576-1
DYNC1I1
NM_001278421.2
c.365+54_365+56delAAA
intron
N/ANP_001265350.1O14576-5

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DYNC1I1
ENST00000447467.6
TSL:1 MANE Select
c.314+42_314+44delAAA
intron
N/AENSP00000392337.2O14576-2
DYNC1I1
ENST00000324972.10
TSL:1
c.365+42_365+44delAAA
intron
N/AENSP00000320130.6O14576-1
DYNC1I1
ENST00000457059.2
TSL:1
c.314+42_314+44delAAA
intron
N/AENSP00000412444.1O14576-2

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
141094
Hom.:
0
Cov.:
0
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000434
AC:
55
AN:
1267224
Hom.:
0
AF XY:
0.0000334
AC XY:
21
AN XY:
627888
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0000369
AC:
1
AN:
27070
American (AMR)
AF:
0.0000404
AC:
1
AN:
24780
Ashkenazi Jewish (ASJ)
AF:
0.000241
AC:
5
AN:
20778
East Asian (EAS)
AF:
0.0000283
AC:
1
AN:
35304
South Asian (SAS)
AF:
0.000117
AC:
8
AN:
68210
European-Finnish (FIN)
AF:
0.000121
AC:
5
AN:
41436
Middle Eastern (MID)
AF:
0.000204
AC:
1
AN:
4900
European-Non Finnish (NFE)
AF:
0.0000323
AC:
32
AN:
992226
Other (OTH)
AF:
0.0000190
AC:
1
AN:
52520
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.245
Heterozygous variant carriers
0
8
17
25
34
42
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
141094
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
68100
African (AFR)
AF:
0.00
AC:
0
AN:
38738
American (AMR)
AF:
0.00
AC:
0
AN:
14128
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3312
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4838
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4424
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
7896
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
300
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
64642
Other (OTH)
AF:
0.00
AC:
0
AN:
1942

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.30

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

Other links and lift over

dbSNP: rs35397709; hg19: chr7-95442690; API