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: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, ClinGen, 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO18B	XM_011530461.3	c.*5813A>G		3_prime_UTR_variant	Exon 45 of 45		XP_011528763.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;