rs533064

chr18-49865518-A-T

Variant summary

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

The NM_001080467.3(MYO5B):c.3604-1138T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,090 control chromosomes in the GnomAD database, including 14,611 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 0.43 (14611 hom., cov: 32)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO5B	NM_001080467.3	c.3604-1138T>A		intron_variant		ENST00000285039.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO5B	ENST00000285039.12	c.3604-1138T>A		intron_variant		1	NM_001080467.3	P1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65247 AN: 151972 Hom.: 14616 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.429 AC: 65247 AN: 152090 Hom.: 14611 Cov.: 32 AF XY: 0.424 AC XY: 31542 AN XY: 74336

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.468

Alfa AF: 0.454 Hom.: 1971

Bravo AF: 0.422

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.6
Dann	Benign	0.85

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: rs533064; hg19: chr18-47391888;