22-25761342-G-C

Position:

• chr22-25761342-G-C

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.39+211G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (331 hom., cov: 0)
• Consequence: MYO18B NM_032608.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.71

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=-0.97).
• BP6: Variant 22-25761342-G-C is Benign according to our data. Variant chr22-25761342-G-C is described in ClinVar as [Benign]. Clinvar id is 1256908.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO18B	NM_032608.7	c.39+211G>C		intron_variant		ENST00000335473.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO18B	ENST00000335473.12	c.39+211G>C		intron_variant		1	NM_032608.7	A2
MYO18B	ENST00000407587.6	c.39+211G>C		intron_variant		1		P5
MYO18B	ENST00000536101.5	c.39+211G>C		intron_variant		1		A2
MYO18B	ENST00000539302.5	c.39+211G>C		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 5490 AN: 41770 Hom.: 331 Cov.: 0

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0608

Gnomad ASJ AF: 0.00123

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0218

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0196

Gnomad NFE AF: 0.00208

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.132 AC: 5503 AN: 41792 Hom.: 331 Cov.: 0 AF XY: 0.129 AC XY: 2604 AN XY: 20188

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.0608

Gnomad4 ASJ AF: 0.00123

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.0219

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00208

Gnomad4 OTH AF: 0.0901

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

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.33
DANN	Benign	0.24

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: rs133878; hg19: chr22-26157309;