rs1787292

Positions:

• chr18-49898744-T-C
• chr18-49898744-T-G

Variant summary

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

The NM_001080467.3(MYO5B):​c.2812-3570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,954 control chromosomes in the GnomAD database, including 25,932 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 0.58 (25932 hom., cov: 32)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO5B	NM_001080467.3	c.2812-3570A>G		intron_variant		ENST00000285039.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO5B	ENST00000285039.12	c.2812-3570A>G		intron_variant		1	NM_001080467.3	P1
MYO5B	ENST00000324581.10	c.241-3570A>G		intron_variant		2
MYO5B	ENST00000697219.1	c.2609-3570A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88416 AN: 151836 Hom.: 25924 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.582 AC: 88464 AN: 151954 Hom.: 25932 Cov.: 32 AF XY: 0.582 AC XY: 43190 AN XY: 74244

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.619

Alfa AF: 0.604 Hom.: 4738

Bravo AF: 0.588

Asia WGS AF: 0.562 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.72

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: rs1787292; hg19: chr18-47425114;