Variant 22-25877922-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_032608.7(MYO18B):c.4225-37C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 1,525,914 control chromosomes in the GnomAD database, including 80,684 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 9543 hom., cov: 33)

Exomes 𝑓: 0.32 ( 71141 hom. )

Consequence

MYO18B
NM_032608.7 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.951

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:

MYO18B (HGNC:):

MYO18B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 22-25877922-C-T is Benign according to our data. Variant chr22-25877922-C-T is described in ClinVar as [Benign]. Clinvar id is 1242816.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO18B	NM_032608.7 linkuse as main transcript	c.4225-37C>T		intron_variant		ENST00000335473.12	NP_115997.5	Q8IUG5-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
MYO18B	ENST00000335473.12 linkuse as main transcript	c.4225-37C>T	intron_variant	1	NM_032608.7	ENSP00000334563.8	Q8IUG5-1
MYO18B	ENST00000407587.6 linkuse as main transcript	c.4228-37C>T	intron_variant	1		ENSP00000386096.2	Q8IUG5-3
MYO18B	ENST00000536101.5 linkuse as main transcript	c.4225-37C>T	intron_variant	1		ENSP00000441229.1	Q8IUG5-1
MYO18B	ENST00000539302.5 linkuse as main transcript	n.*1683-37C>T	intron_variant	1		ENSP00000437587.1	F5H6I8

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52343

AN:

151932

Hom.:

9525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.334

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.333

GnomAD3 exomes

AF:

0.318

AC:

51061

AN:

160470

Hom.:

8692

AF XY:

0.322

AC XY:

27170

AN XY:

84388

show subpopulations

Gnomad AFR exome

AF:

0.452

Gnomad AMR exome

AF:

0.198

Gnomad ASJ exome

AF:

0.257

Gnomad EAS exome

AF:

0.514

Gnomad SAS exome

AF:

0.349

Gnomad FIN exome

AF:

0.332

Gnomad NFE exome

AF:

0.306

Gnomad OTH exome

AF:

0.315

GnomAD4 exome

AF:

0.318

AC:

437102

AN:

1373862

Hom.:

71141

Cov.:

AF XY:

0.318

AC XY:

216040

AN XY:

679316

show subpopulations

Gnomad4 AFR exome

AF:

0.455

Gnomad4 AMR exome

AF:

0.204

Gnomad4 ASJ exome

AF:

0.258

Gnomad4 EAS exome

AF:

0.479

Gnomad4 SAS exome

AF:

0.349

Gnomad4 FIN exome

AF:

0.332

Gnomad4 NFE exome

AF:

0.310

Gnomad4 OTH exome

AF:

0.337

GnomAD4 genome

AF:

0.345

AC:

52400

AN:

152052

Hom.:

9543

Cov.:

AF XY:

0.345

AC XY:

25638

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.436

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.259

Gnomad4 EAS

AF:

0.495

Gnomad4 SAS

AF:

0.353

Gnomad4 FIN

AF:

0.334

Gnomad4 NFE

AF:

0.307

Gnomad4 OTH

AF:

0.338

Alfa

AF:

0.312

Hom.:

1988

Bravo

AF:

0.343

Asia WGS

AF:

0.412

AC:

1432

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 submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.10

DANN

Benign

0.67

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