rs5752249

Positions:

• chr22-25992740-G-A
• chr22-25992740-G-C
• chr22-25992740-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032608.7(MYO18B):​c.6287+247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 152,282 control chromosomes in the GnomAD database, including 656 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.063 (656 hom., cov: 33)
• Consequence: MYO18B NM_032608.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0110

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 22-25992740-G-A is Benign according to our data. Variant chr22-25992740-G-A is described in ClinVar as [Benign]. Clinvar id is 1231212.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO18B	NM_032608.7	c.6287+247G>A		intron_variant		ENST00000335473.12	NP_115997.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO18B	ENST00000335473.12	c.6287+247G>A		intron_variant		1	NM_032608.7	ENSP00000334563	A2

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9645 AN: 152164 Hom.: 655 Cov.: 33

Gnomad AFR AF: 0.0130

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.0696

Gnomad FIN AF: 0.0953

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0453

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0634 AC: 9651 AN: 152282 Hom.: 656 Cov.: 33 AF XY: 0.0701 AC XY: 5221 AN XY: 74450

Gnomad4 AFR AF: 0.0130

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.0695

Gnomad4 FIN AF: 0.0953

Gnomad4 NFE AF: 0.0453

Gnomad4 OTH AF: 0.0818

Alfa AF: 0.0583 Hom.: 438

Bravo AF: 0.0701

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.39

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: rs5752249; hg19: chr22-26388706;