rs1705533

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080467.3(MYO5B):​c.28-68445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,032 control chromosomes in the GnomAD database, including 28,674 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 0.61 ( 28674 hom., cov: 32)

Consequence

MYO5B
NM_001080467.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.878
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYO5BNM_001080467.3 linkuse as main transcriptc.28-68445C>T intron_variant ENST00000285039.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYO5BENST00000285039.12 linkuse as main transcriptc.28-68445C>T intron_variant 1 NM_001080467.3 P1Q9ULV0-1
MYO5BENST00000697221.1 linkuse as main transcriptn.399-68445C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.613
AC:
93097
AN:
151914
Hom.:
28654
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.613
Gnomad AMI
AF:
0.691
Gnomad AMR
AF:
0.693
Gnomad ASJ
AF:
0.614
Gnomad EAS
AF:
0.636
Gnomad SAS
AF:
0.647
Gnomad FIN
AF:
0.567
Gnomad MID
AF:
0.586
Gnomad NFE
AF:
0.596
Gnomad OTH
AF:
0.632
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.613
AC:
93161
AN:
152032
Hom.:
28674
Cov.:
32
AF XY:
0.614
AC XY:
45615
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.613
Gnomad4 AMR
AF:
0.694
Gnomad4 ASJ
AF:
0.614
Gnomad4 EAS
AF:
0.636
Gnomad4 SAS
AF:
0.647
Gnomad4 FIN
AF:
0.567
Gnomad4 NFE
AF:
0.596
Gnomad4 OTH
AF:
0.632
Alfa
AF:
0.604
Hom.:
51736
Bravo
AF:
0.621
Asia WGS
AF:
0.678
AC:
2356
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.12
DANN
Benign
0.51

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1705533; hg19: chr18-47650193; API