chr22-25761341-CG-C

Variant names:

• chr22-25761341-CG-C
• rs139553322
• NM_032608.7:c.39+211delG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.71
• Publications: 0 publications found

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYO18B	NM_032608.7	c.39+211delG		intron_variant	Intron 2 of 43	ENST00000335473.12	NP_115997.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO18B	ENST00000335473.12	c.39+211delG		intron_variant	Intron 2 of 43	1	NM_032608.7	ENSP00000334563.8
MYO18B	ENST00000407587.6	c.39+211delG		intron_variant	Intron 2 of 43	1		ENSP00000386096.2
MYO18B	ENST00000536101.5	c.39+211delG		intron_variant	Intron 2 of 42	1		ENSP00000441229.1
MYO18B	ENST00000539302.5	n.39+211delG		intron_variant	Intron 1 of 41	1		ENSP00000437587.1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83024 AN: 150980 Hom.: 24195 Cov.: 0

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.: 0 AF XY: 0.553 AC XY: 40828 AN XY: 73832

African (AFR) AF: 0.733 AC: 29903 AN: 40774

American (AMR) AF: 0.595 AC: 9042 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1811 AN: 3466

East Asian (EAS) AF: 0.824 AC: 4229 AN: 5130

South Asian (SAS) AF: 0.553 AC: 2649 AN: 4788

European-Finnish (FIN) AF: 0.424 AC: 4481 AN: 10556

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29498 AN: 67884

Other (OTH) AF: 0.542 AC: 1137 AN: 2098

Alfa AF: 0.256 Hom.: 346

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs139553322; hg19: chr22-26157308;