GeneBe

rs11452827

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.224-144_224-140delTTTTT variant causes a intron change. The variant allele was found at a frequency of 0.00000103 in 973,924 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: not found (cov: 0)
Exomes 𝑓: 0.0000010 ( 0 hom. )

Consequence

DYNC1I1
NM_001135556.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.39

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.224-144_224-140delTTTTT
intron
N/ANP_001129028.1O14576-2
DYNC1I1
NM_004411.5
c.224-93_224-89delTTTTT
intron
N/ANP_004402.1O14576-1
DYNC1I1
NM_001278421.2
c.224-93_224-89delTTTTT
intron
N/ANP_001265350.1O14576-5

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DYNC1I1
ENST00000447467.6
TSL:1 MANE Select
c.224-153_224-149delTTTTT
intron
N/AENSP00000392337.2O14576-2
DYNC1I1
ENST00000324972.10
TSL:1
c.224-102_224-98delTTTTT
intron
N/AENSP00000320130.6O14576-1
DYNC1I1
ENST00000457059.2
TSL:1
c.224-153_224-149delTTTTT
intron
N/AENSP00000412444.1O14576-2

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000103
AC:
1
AN:
973924
Hom.:
0
AF XY:
0.00000206
AC XY:
1
AN XY:
484630
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
18796
American (AMR)
AF:
0.00
AC:
0
AN:
17456
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
16878
East Asian (EAS)
AF:
0.00
AC:
0
AN:
26528
South Asian (SAS)
AF:
0.0000203
AC:
1
AN:
49364
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
30472
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2948
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
771070
Other (OTH)
AF:
0.00
AC:
0
AN:
40412
⚠️ 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: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
4.4

Splicing

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

Publications

Other links and lift over

dbSNP: rs11452827; hg19: chr7-95442405; API