chr22-25998758-A-G

Position:

• chr22-25998758-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032608.7(MYO18B):​c.6288-4507A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,878 control chromosomes in the GnomAD database, including 23,196 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 0.52 (23196 hom., cov: 32)
• Consequence: MYO18B NM_032608.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO18B	NM_032608.7	c.6288-4507A>G		intron_variant		ENST00000335473.12	NP_115997.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO18B	ENST00000335473.12	c.6288-4507A>G		intron_variant		1	NM_032608.7	ENSP00000334563	A2

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79023 AN: 151760 Hom.: 23167 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.521 AC: 79099 AN: 151878 Hom.: 23196 Cov.: 32 AF XY: 0.507 AC XY: 37635 AN XY: 74232

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.488

Alfa AF: 0.470 Hom.: 37261

Bravo AF: 0.541

Asia WGS AF: 0.253 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.039
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

Other links and lift over

dbSNP: rs8139900; hg19: chr22-26394724; COSMIC: COSV59136077;