18-49929610-GAAAAAAA-GAAAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS1

The NM_001080467.3(MYO5B):​c.2004-15_2004-13delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00436 in 1,260,590 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: 𝑓 0.000060 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0049 ( 0 hom. )

Consequence

MYO5B
NM_001080467.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.06
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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00487 (5489/1127764) while in subpopulation AMR AF= 0.00723 (227/31410). AF 95% confidence interval is 0.00646. There are 0 homozygotes in gnomad4_exome. There are 2565 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MYO5BNM_001080467.3 linkc.2004-15_2004-13delTTT intron_variant Intron 16 of 39 ENST00000285039.12 NP_001073936.1 Q9ULV0-1Q7Z7A5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYO5BENST00000285039.12 linkc.2004-15_2004-13delTTT intron_variant Intron 16 of 39 1 NM_001080467.3 ENSP00000285039.6 Q9ULV0-1
MYO5BENST00000697219.1 linkc.1800-15_1800-13delTTT intron_variant Intron 14 of 37 ENSP00000513188.1 A0A8V8TM52

Frequencies

GnomAD3 genomes
AF:
0.0000602
AC:
8
AN:
132848
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000565
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000152
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000145
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000480
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00734
AC:
840
AN:
114366
Hom.:
0
AF XY:
0.00712
AC XY:
439
AN XY:
61680
show subpopulations
Gnomad AFR exome
AF:
0.00579
Gnomad AMR exome
AF:
0.00885
Gnomad ASJ exome
AF:
0.00402
Gnomad EAS exome
AF:
0.00755
Gnomad SAS exome
AF:
0.00679
Gnomad FIN exome
AF:
0.0137
Gnomad NFE exome
AF:
0.00661
Gnomad OTH exome
AF:
0.00675
GnomAD4 exome
AF:
0.00487
AC:
5489
AN:
1127764
Hom.:
0
AF XY:
0.00455
AC XY:
2565
AN XY:
563876
show subpopulations
Gnomad4 AFR exome
AF:
0.00531
Gnomad4 AMR exome
AF:
0.00723
Gnomad4 ASJ exome
AF:
0.00378
Gnomad4 EAS exome
AF:
0.00341
Gnomad4 SAS exome
AF:
0.00421
Gnomad4 FIN exome
AF:
0.00467
Gnomad4 NFE exome
AF:
0.00492
Gnomad4 OTH exome
AF:
0.00475
GnomAD4 genome
AF:
0.0000602
AC:
8
AN:
132826
Hom.:
0
Cov.:
0
AF XY:
0.0000630
AC XY:
4
AN XY:
63444
show subpopulations
Gnomad4 AFR
AF:
0.0000564
Gnomad4 AMR
AF:
0.000152
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000145
Gnomad4 NFE
AF:
0.0000480
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs56278513; hg19: chr18-47455980; API