chr18-49919037-C-T

Variant names:

• chr18-49919037-C-T
• rs1787534
• NM_001080467.3:c.2091-6864G>A

Variant summary

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

The NM_001080467.3(MYO5B):​c.2091-6864G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,154 control chromosomes in the GnomAD database, including 1,493 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 (1493 hom., cov: 33)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO5B	NM_001080467.3	c.2091-6864G>A		intron_variant	Intron 17 of 39	ENST00000285039.12	NP_001073936.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO5B	ENST00000285039.12	c.2091-6864G>A		intron_variant	Intron 17 of 39	1	NM_001080467.3	ENSP00000285039.6
MYO5B	ENST00000697219.1	c.1887-6864G>A		intron_variant	Intron 15 of 37			ENSP00000513188.1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19294 AN: 152036 Hom.: 1491 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0890

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.127 AC: 19313 AN: 152154 Hom.: 1493 Cov.: 33 AF XY: 0.127 AC XY: 9442 AN XY: 74404

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.0625

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0890

Gnomad4 OTH AF: 0.0995

Alfa AF: 0.0870 Hom.: 855

Bravo AF: 0.124

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.54
DANN	Benign	0.71

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: rs1787534; hg19: chr18-47445407;