NM_001080467.3:c.1753-3722C>A

Variant names:

• chr18-49941119-G-T
• rs1787603
• NM_001080467.3:c.1753-3722C>A

Variant summary

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

The NM_001080467.3(MYO5B):​c.1753-3722C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,974 control chromosomes in the GnomAD database, including 26,531 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 0.59 (26531 hom., cov: 31)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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 (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO5B	NM_001080467.3	c.1753-3722C>A		intron_variant	Intron 14 of 39	ENST00000285039.12	NP_001073936.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO5B	ENST00000285039.12	c.1753-3722C>A		intron_variant	Intron 14 of 39	1	NM_001080467.3	ENSP00000285039.6
MYO5B	ENST00000697219.1	c.1549-3722C>A		intron_variant	Intron 12 of 37			ENSP00000513188.1

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88872 AN: 151854 Hom.: 26515 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.585 AC: 88938 AN: 151974 Hom.: 26531 Cov.: 31 AF XY: 0.576 AC XY: 42766 AN XY: 74256

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.605

Alfa AF: 0.483 Hom.: 2085

Bravo AF: 0.592

Asia WGS AF: 0.423 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.58

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: rs1787603; hg19: chr18-47467489;