22-25761379-AGGT-A

Variant names:

• chr22-25761379-AGGT-A
• NM_032608.7:c.39+266_39+268delTGG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_032608.7(MYO18B):​c.39+266_39+268delTGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,320 control chromosomes in the GnomAD database, including 4,614 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (4614 hom., cov: 24)
• Consequence: MYO18B NM_032608.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.138

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 -10 ACMG points.

• BP6: Variant 22-25761379-AGGT-A is Benign according to our data. Variant chr22-25761379-AGGT-A is described in ClinVar as [Benign]. Clinvar id is 1295960.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO18B	NM_032608.7	c.39+266_39+268delTGG		intron_variant	Intron 2 of 43	ENST00000335473.12	NP_115997.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO18B	ENST00000335473.12	c.39+249_39+251delGGT		intron_variant	Intron 2 of 43	1	NM_032608.7	ENSP00000334563.8
MYO18B	ENST00000407587.6	c.39+249_39+251delGGT		intron_variant	Intron 2 of 43	1		ENSP00000386096.2
MYO18B	ENST00000536101.5	c.39+249_39+251delGGT		intron_variant	Intron 2 of 42	1		ENSP00000441229.1
MYO18B	ENST00000539302.5	n.39+249_39+251delGGT		intron_variant	Intron 1 of 41	1		ENSP00000437587.1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36313 AN: 151198 Hom.: 4596 Cov.: 24

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.240 AC: 36353 AN: 151320 Hom.: 4614 Cov.: 24 AF XY: 0.235 AC XY: 17402 AN XY: 73902

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.242

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 21, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-26157346;