22-25877883-G-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032608.7(MYO18B):​c.4225-76G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 1,244,174 control chromosomes in the GnomAD database, including 396,163 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.81 ( 50230 hom., cov: 33)
Exomes 𝑓: 0.79 ( 345933 hom. )

Consequence

MYO18B
NM_032608.7 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.138
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
Variant 22-25877883-G-C is Benign according to our data. Variant chr22-25877883-G-C is described in ClinVar as [Benign]. Clinvar id is 1288011.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYO18BNM_032608.7 linkuse as main transcriptc.4225-76G>C intron_variant ENST00000335473.12 NP_115997.5 Q8IUG5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MYO18BENST00000335473.12 linkuse as main transcriptc.4225-76G>C intron_variant 1 NM_032608.7 ENSP00000334563.8 Q8IUG5-1
MYO18BENST00000407587.6 linkuse as main transcriptc.4228-76G>C intron_variant 1 ENSP00000386096.2 Q8IUG5-3
MYO18BENST00000536101.5 linkuse as main transcriptc.4225-76G>C intron_variant 1 ENSP00000441229.1 Q8IUG5-1
MYO18BENST00000539302.5 linkuse as main transcriptn.*1683-76G>C intron_variant 1 ENSP00000437587.1 F5H6I8

Frequencies

GnomAD3 genomes
AF:
0.810
AC:
123143
AN:
152118
Hom.:
50175
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.849
Gnomad AMI
AF:
0.745
Gnomad AMR
AF:
0.813
Gnomad ASJ
AF:
0.661
Gnomad EAS
AF:
0.997
Gnomad SAS
AF:
0.876
Gnomad FIN
AF:
0.834
Gnomad MID
AF:
0.778
Gnomad NFE
AF:
0.772
Gnomad OTH
AF:
0.770
GnomAD4 exome
AF:
0.794
AC:
867210
AN:
1091938
Hom.:
345933
AF XY:
0.795
AC XY:
436288
AN XY:
548580
show subpopulations
Gnomad4 AFR exome
AF:
0.853
Gnomad4 AMR exome
AF:
0.864
Gnomad4 ASJ exome
AF:
0.656
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.862
Gnomad4 FIN exome
AF:
0.823
Gnomad4 NFE exome
AF:
0.778
Gnomad4 OTH exome
AF:
0.790
GnomAD4 genome
AF:
0.810
AC:
123259
AN:
152236
Hom.:
50230
Cov.:
33
AF XY:
0.815
AC XY:
60619
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.849
Gnomad4 AMR
AF:
0.814
Gnomad4 ASJ
AF:
0.661
Gnomad4 EAS
AF:
0.997
Gnomad4 SAS
AF:
0.876
Gnomad4 FIN
AF:
0.834
Gnomad4 NFE
AF:
0.772
Gnomad4 OTH
AF:
0.773
Alfa
AF:
0.721
Hom.:
2122
Bravo
AF:
0.810
Asia WGS
AF:
0.931
AC:
3237
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxNov 12, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
5.4
DANN
Benign
0.29

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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: rs695428; hg19: chr22-26273850; API