GeneBe

rs56278513

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001080467.3(MYO5B):​c.2004-19_2004-13delTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000865 in 1,155,606 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 8.7e-7 ( 0 hom. )

Consequence

MYO5B
NM_001080467.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.06

Publications

0 publications found
Variant links:
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

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MYO5BNM_001080467.3 linkc.2004-19_2004-13delTTTTTTT intron_variant Intron 16 of 39 ENST00000285039.12 NP_001073936.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYO5BENST00000285039.12 linkc.2004-19_2004-13delTTTTTTT intron_variant Intron 16 of 39 1 NM_001080467.3 ENSP00000285039.6
MYO5BENST00000697219.1 linkc.1800-19_1800-13delTTTTTTT intron_variant Intron 14 of 37 ENSP00000513188.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
8.65e-7
AC:
1
AN:
1155606
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
577646
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
26604
American (AMR)
AF:
0.0000312
AC:
1
AN:
32072
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22244
East Asian (EAS)
AF:
0.00
AC:
0
AN:
33536
South Asian (SAS)
AF:
0.00
AC:
0
AN:
70378
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
36188
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3522
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
882018
Other (OTH)
AF:
0.00
AC:
0
AN:
49044
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs56278513; hg19: chr18-47455980; API