16-15703925-GTTTTT-GTTTTTT
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_002474.3(MYH11):c.*65dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00498 in 1,606,278 control chromosomes in the GnomAD database, including 333 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.027 ( 178 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 155 hom. )
Consequence
MYH11
NM_002474.3 3_prime_UTR
NM_002474.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.794
Publications
1 publications found
Genes affected
MYH11 (HGNC:7569): (myosin heavy chain 11) The protein encoded by this gene is a smooth muscle myosin belonging to the myosin heavy chain family. The gene product is a subunit of a hexameric protein that consists of two heavy chain subunits and two pairs of non-identical light chain subunits. It functions as a major contractile protein, converting chemical energy into mechanical energy through the hydrolysis of ATP. A chromosomal rearrangement involving this gene is associated with acute myeloid leukemia of the M4Eo subtype. Mutations in this gene are associated with visceral myopathy, megacystis-microcolon-intestinal hypoperistalsis syndrome 2, and familial thoracic aortic aneurysm 4. [provided by RefSeq, May 2022]
NDE1 (HGNC:17619): (nudE neurodevelopment protein 1) This gene encodes a member of the nuclear distribution E (NudE) family of proteins. The encoded protein is localized at the centrosome and interacts with other centrosome components as part of a multiprotein complex that regulates dynein function. This protein plays an essential role in microtubule organization, mitosis and neuronal migration. Mutations in this gene cause lissencephaly 4, a disorder characterized by lissencephaly, severe brain atrophy, microcephaly, and severe cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]
NDE1 Gene-Disease associations (from GenCC):
- lissencephaly 4Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: PanelApp Australia, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine
- hydranencephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- microlissencephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- NDE1-related microhydranencephalyInheritance: Unknown, AR Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 16-15703925-G-GT is Benign according to our data. Variant chr16-15703925-G-GT is described in ClinVar as [Benign]. Clinvar id is 1294395.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0924 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH11 | NM_002474.3 | c.*65dupA | 3_prime_UTR_variant | Exon 41 of 41 | ENST00000300036.6 | NP_002465.1 | ||
MYH11 | NM_001040113.2 | c.*206dupA | 3_prime_UTR_variant | Exon 43 of 43 | ENST00000452625.7 | NP_001035202.1 | ||
NDE1 | NM_017668.3 | c.947+7073dupT | intron_variant | Intron 8 of 8 | ENST00000396354.6 | NP_060138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH11 | ENST00000300036.6 | c.*65dupA | 3_prime_UTR_variant | Exon 41 of 41 | 1 | NM_002474.3 | ENSP00000300036.5 | |||
MYH11 | ENST00000452625.7 | c.*206dupA | 3_prime_UTR_variant | Exon 43 of 43 | 1 | NM_001040113.2 | ENSP00000407821.2 | |||
NDE1 | ENST00000396354.6 | c.947+7073dupT | intron_variant | Intron 8 of 8 | 1 | NM_017668.3 | ENSP00000379642.1 |
Frequencies
GnomAD3 genomes AF: 0.0270 AC: 4098AN: 151678Hom.: 178 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
4098
AN:
151678
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00697 AC: 1742AN: 249778 AF XY: 0.00520 show subpopulations
GnomAD2 exomes
AF:
AC:
1742
AN:
249778
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00267 AC: 3889AN: 1454482Hom.: 155 Cov.: 30 AF XY: 0.00226 AC XY: 1634AN XY: 723972 show subpopulations
GnomAD4 exome
AF:
AC:
3889
AN:
1454482
Hom.:
Cov.:
30
AF XY:
AC XY:
1634
AN XY:
723972
show subpopulations
African (AFR)
AF:
AC:
3093
AN:
33286
American (AMR)
AF:
AC:
240
AN:
44672
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
26078
East Asian (EAS)
AF:
AC:
4
AN:
39574
South Asian (SAS)
AF:
AC:
26
AN:
85800
European-Finnish (FIN)
AF:
AC:
1
AN:
53034
Middle Eastern (MID)
AF:
AC:
14
AN:
5672
European-Non Finnish (NFE)
AF:
AC:
151
AN:
1106286
Other (OTH)
AF:
AC:
359
AN:
60080
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.446
Heterozygous variant carriers
0
175
351
526
702
877
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0271 AC: 4110AN: 151796Hom.: 178 Cov.: 32 AF XY: 0.0257 AC XY: 1905AN XY: 74206 show subpopulations
GnomAD4 genome
AF:
AC:
4110
AN:
151796
Hom.:
Cov.:
32
AF XY:
AC XY:
1905
AN XY:
74206
show subpopulations
African (AFR)
AF:
AC:
3921
AN:
41324
American (AMR)
AF:
AC:
141
AN:
15232
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
1
AN:
5166
South Asian (SAS)
AF:
AC:
0
AN:
4786
European-Finnish (FIN)
AF:
AC:
0
AN:
10546
Middle Eastern (MID)
AF:
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11
AN:
67956
Other (OTH)
AF:
AC:
35
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
186
372
559
745
931
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 11, 2019
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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