18-49890700-A-G

Variant names:

• chr18-49890700-A-G
• rs17800754
• NM_001080467.3:c.3045+4241T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080467.3(MYO5B):​c.3045+4241T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,942 control chromosomes in the GnomAD database, including 25,810 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 (25810 hom., cov: 32)
• Consequence: MYO5B NM_001080467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 3 publications found

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]

MYO5B Gene-Disease associations (from GenCC):

• microvillus inclusion disease

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
• cholestasis, progressive familial intrahepatic, 10

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• progressive familial intrahepatic cholestasis type 1

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO5B	NM_001080467.3	c.3045+4241T>C		intron_variant	Intron 22 of 39	ENST00000285039.12	NP_001073936.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO5B	ENST00000285039.12	c.3045+4241T>C		intron_variant	Intron 22 of 39	1	NM_001080467.3	ENSP00000285039.6
MYO5B	ENST00000697219.1	c.2841+4241T>C		intron_variant	Intron 20 of 37			ENSP00000513188.1
MYO5B	ENST00000324581.10	c.474+4241T>C		intron_variant	Intron 2 of 18	2		ENSP00000315531.7

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88259 AN: 151824 Hom.: 25802 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.581 AC: 88307 AN: 151942 Hom.: 25810 Cov.: 32 AF XY: 0.581 AC XY: 43090 AN XY: 74216

African (AFR) AF: 0.511 AC: 21145 AN: 41420

American (AMR) AF: 0.632 AC: 9652 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2257 AN: 3468

East Asian (EAS) AF: 0.535 AC: 2760 AN: 5156

South Asian (SAS) AF: 0.564 AC: 2713 AN: 4812

European-Finnish (FIN) AF: 0.545 AC: 5745 AN: 10544

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41859 AN: 67956

Other (OTH) AF: 0.619 AC: 1309 AN: 2114

Alfa AF: 0.594 Hom.: 4654

Bravo AF: 0.587

Asia WGS AF: 0.563 AC: 1958 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.36
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17800754; hg19: chr18-47417070;