rs2292382

Positions:

• chr18-50098567-G-T

Variant summary

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

The NM_001080467.3(MYO5B):​c.28-43189C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,178 control chromosomes in the GnomAD database, including 1,352 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 0.13 (1352 hom., cov: 33)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO5B	NM_001080467.3	c.28-43189C>A		intron_variant		ENST00000285039.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO5B	ENST00000285039.12	c.28-43189C>A		intron_variant		1	NM_001080467.3	P1
MYO5B	ENST00000697221.1	n.399-43189C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19642 AN: 152060 Hom.: 1341 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.129 AC: 19697 AN: 152178 Hom.: 1352 Cov.: 33 AF XY: 0.130 AC XY: 9665 AN XY: 74398

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.124

Alfa AF: 0.132 Hom.: 768

Bravo AF: 0.128

Asia WGS AF: 0.243 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.69

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: rs2292382; hg19: chr18-47624937;