rs5761313

chr22-25917778-G-T

Variant summary

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

The NM_032608.7(MYO18B):c.5365-3479G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,866 control chromosomes in the GnomAD database, including 11,443 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 0.38 (11443 hom., cov: 32)
• Consequence: MYO18B NM_032608.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO18B	NM_032608.7	c.5365-3479G>T		intron_variant		ENST00000335473.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO18B	ENST00000335473.12	c.5365-3479G>T		intron_variant		1	NM_032608.7	A2

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57667 AN: 151750 Hom.: 11431 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.380 AC: 57705 AN: 151866 Hom.: 11443 Cov.: 32 AF XY: 0.369 AC XY: 27367 AN XY: 74210

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.398

Alfa AF: 0.411 Hom.: 26949

Bravo AF: 0.388

Asia WGS AF: 0.264 AC: 917 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.93
Dann	Benign	0.33

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: rs5761313; hg19: chr22-26313745;