rs9613094

Positions:

• chr22-26062422-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MYO18B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MYO18B	XM_011530461.3	c.*5813A>G		3_prime_UTR_variant	45/45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.210

Alfa AF: 0.209 Hom.: 4643

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9613094; hg19: chr22-26458388;