rs9613094

Variant names:

• chr22-26062422-A-G
• rs9613094
• XM_011530461.3:c.*5813A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011530461.3(MYO18B):​c.*5813A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,014 control chromosomes in the GnomAD database, including 3,328 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3328 hom., cov: 31)
• Consequence: MYO18B XM_011530461.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 3 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: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31221 AN: 151894 Hom.: 3321 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.205 AC: 31235 AN: 152014 Hom.: 3328 Cov.: 31 AF XY: 0.207 AC XY: 15387 AN XY: 74292

African (AFR) AF: 0.191 AC: 7939 AN: 41468

American (AMR) AF: 0.179 AC: 2729 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1123 AN: 5144

South Asian (SAS) AF: 0.249 AC: 1197 AN: 4806

European-Finnish (FIN) AF: 0.227 AC: 2397 AN: 10574

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14175 AN: 67956

Other (OTH) AF: 0.210 AC: 444 AN: 2114

Alfa AF: 0.208 Hom.: 6297

Bravo AF: 0.202

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.048
DANN	Benign	0.47
PhyloP100		-0.035

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9613094; hg19: chr22-26458388;