Variant 22-25761341-CG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_032608.7(MYO18B):c.39+211delG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.55 ( 24257 hom., cov: 0)

Consequence

MYO18B
NM_032608.7 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.71

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 22-25761341-CG-C is Benign according to our data. Variant chr22-25761341-CG-C is described in ClinVar as [Benign]. Clinvar id is 1278433.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO18B	NM_032608.7 link	c.39+211delG		intron_variant		ENST00000335473.12	NP_115997.5	Q8IUG5-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
MYO18B	ENST00000335473.12 link	c.39+211delG	intron_variant	1	NM_032608.7	ENSP00000334563.8	Q8IUG5-1
MYO18B	ENST00000407587.6 link	c.39+211delG	intron_variant	1		ENSP00000386096.2	Q8IUG5-3
MYO18B	ENST00000536101.5 link	c.39+211delG	intron_variant	1		ENSP00000441229.1	Q8IUG5-1
MYO18B	ENST00000539302.5 link	n.39+211delG	intron_variant	1		ENSP00000437587.1	F5H6I8

Frequencies

GnomAD3 genomes

AF:

0.550

AC:

83024

AN:

150980

Hom.:

24195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.733

Gnomad AMI

AF:

0.278

Gnomad AMR

AF:

0.594

Gnomad ASJ

AF:

0.523

Gnomad EAS

AF:

0.824

Gnomad SAS

AF:

0.552

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.435

Gnomad OTH

AF:

0.540

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.550

AC:

83147

AN:

151100

Hom.:

24257

Cov.:

AF XY:

0.553

AC XY:

40828

AN XY:

73832

show subpopulations

Gnomad4 AFR

AF:

0.733

Gnomad4 AMR

AF:

0.595

Gnomad4 ASJ

AF:

0.523

Gnomad4 EAS

AF:

0.824

Gnomad4 SAS

AF:

0.553

Gnomad4 FIN

AF:

0.424

Gnomad4 NFE

AF:

0.435

Gnomad4 OTH

AF:

0.542

Alfa

AF:

0.256

Hom.:

346

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over