rs1787566

chr18-49881833-C-T

Variant summary

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

The NM_001080467.3(MYO5B):c.3046-1378G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 151,242 control chromosomes in the GnomAD database, including 54,482 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 0.85 (54482 hom., cov: 29)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449

Genes affected

MYO5B (HGNC:7603): (myosin VB) The protein encoded by this gene, together with other proteins, may be involved in plasma membrane recycling. Mutations in this gene are associated with microvillous inclusion disease. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO5B	NM_001080467.3	c.3046-1378G>A		intron_variant		ENST00000285039.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO5B	ENST00000285039.12	c.3046-1378G>A		intron_variant		1	NM_001080467.3	P1
MYO5B	ENST00000324581.10	c.475-1378G>A		intron_variant		2
MYO5B	ENST00000697219.1	c.2843-1378G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128170 AN: 151134 Hom.: 54431 Cov.: 29

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.848 AC: 128275 AN: 151242 Hom.: 54482 Cov.: 29 AF XY: 0.853 AC XY: 62903 AN XY: 73754

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.865

Alfa AF: 0.830 Hom.: 23127

Bravo AF: 0.855

Asia WGS AF: 0.933 AC: 3223 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.8
Dann	Benign	0.43

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: rs1787566; hg19: chr18-47408203;