22-25761379-AGGT-A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_032608.7(MYO18B):​c.39+266_39+268delTGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,320 control chromosomes in the GnomAD database, including 4,614 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4614 hom., cov: 24)

Consequence

MYO18B
NM_032608.7 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.138

Publications

0 publications found
Variant links:
Genes affected
MYO18B (HGNC:18150): (myosin XVIIIB) The protein encoded by this gene may regulate muscle-specific genes when in the nucleus and may influence intracellular trafficking when in the cytoplasm. The encoded protein functions as a homodimer and may interact with F actin. Mutations in this gene are associated with lung cancer. [provided by RefSeq, Jul 2008]
MYO18B Gene-Disease associations (from GenCC):
  • Klippel-Feil anomaly-myopathy-facial dysmorphism syndrome
    Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, ClinGen, G2P

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6
Variant 22-25761379-AGGT-A is Benign according to our data. Variant chr22-25761379-AGGT-A is described in ClinVar as [Benign]. Clinvar id is 1295960.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MYO18BNM_032608.7 linkc.39+266_39+268delTGG intron_variant Intron 2 of 43 ENST00000335473.12 NP_115997.5 Q8IUG5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYO18BENST00000335473.12 linkc.39+249_39+251delGGT intron_variant Intron 2 of 43 1 NM_032608.7 ENSP00000334563.8 Q8IUG5-1
MYO18BENST00000407587.6 linkc.39+249_39+251delGGT intron_variant Intron 2 of 43 1 ENSP00000386096.2 Q8IUG5-3
MYO18BENST00000536101.5 linkc.39+249_39+251delGGT intron_variant Intron 2 of 42 1 ENSP00000441229.1 Q8IUG5-1
MYO18BENST00000539302.5 linkn.39+249_39+251delGGT intron_variant Intron 1 of 41 1 ENSP00000437587.1 F5H6I8

Frequencies

GnomAD3 genomes
AF:
0.240
AC:
36313
AN:
151198
Hom.:
4596
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.332
Gnomad AMI
AF:
0.174
Gnomad AMR
AF:
0.196
Gnomad ASJ
AF:
0.285
Gnomad EAS
AF:
0.167
Gnomad SAS
AF:
0.145
Gnomad FIN
AF:
0.165
Gnomad MID
AF:
0.275
Gnomad NFE
AF:
0.216
Gnomad OTH
AF:
0.246
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.240
AC:
36353
AN:
151320
Hom.:
4614
Cov.:
24
AF XY:
0.235
AC XY:
17402
AN XY:
73902
show subpopulations
African (AFR)
AF:
0.332
AC:
13694
AN:
41208
American (AMR)
AF:
0.196
AC:
2986
AN:
15228
Ashkenazi Jewish (ASJ)
AF:
0.285
AC:
986
AN:
3462
East Asian (EAS)
AF:
0.167
AC:
852
AN:
5098
South Asian (SAS)
AF:
0.145
AC:
690
AN:
4766
European-Finnish (FIN)
AF:
0.165
AC:
1722
AN:
10464
Middle Eastern (MID)
AF:
0.282
AC:
83
AN:
294
European-Non Finnish (NFE)
AF:
0.216
AC:
14674
AN:
67796
Other (OTH)
AF:
0.242
AC:
508
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1354
2708
4062
5416
6770
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
366
732
1098
1464
1830
<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:
0.0541
Hom.:
50

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jun 21, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.14
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
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

hg19: chr22-26157346; COSMIC: COSV59128623; COSMIC: COSV59128623; API