Variant rs3841750 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PM4_SupportingBP6_Very_StrongBA1

The NM_001080467.3(MYO5B):c.3165_3166insCTC(p.Leu1055dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 1,613,342 control chromosomes in the GnomAD database, including 78,462 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8240 hom., cov: 0)

Exomes 𝑓: 0.30 ( 70222 hom. )

Consequence

MYO5B
NM_001080467.3 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts P:1B:5

Conservation

PhyloP100: -0.226

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001080467.3. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 18-49879055-T-TGAG is Benign according to our data. Variant chr18-49879055-T-TGAG is described in ClinVar as [Benign]. Clinvar id is 327031.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO5B	NM_001080467.3 linkuse as main transcript	c.3165_3166insCTC	p.Leu1055dup	inframe_insertion	24/40	ENST00000285039.12	NP_001073936.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO5B	ENST00000285039.12 linkuse as main transcript	c.3165_3166insCTC	p.Leu1055dup	inframe_insertion	24/40	1	NM_001080467.3	ENSP00000285039	P1	Q9ULV0-1

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49135

AN:

151762

Hom.:

8235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.363

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.542

Gnomad SAS

AF:

0.501

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.291

GnomAD3 exomes

AF:

0.340

AC:

84825

AN:

249362

Hom.:

15532

AF XY:

0.346

AC XY:

46763

AN XY:

135288

show subpopulations

Gnomad AFR exome

AF:

0.359

Gnomad AMR exome

AF:

0.286

Gnomad ASJ exome

AF:

0.281

Gnomad EAS exome

AF:

0.557

Gnomad SAS exome

AF:

0.495

Gnomad FIN exome

AF:

0.364

Gnomad NFE exome

AF:

0.280

Gnomad OTH exome

AF:

0.316

GnomAD4 exome

AF:

0.302

AC:

441199

AN:

1461462

Hom.:

70222

Cov.:

AF XY:

0.308

AC XY:

223571

AN XY:

727058

show subpopulations

Gnomad4 AFR exome

AF:

0.363

Gnomad4 AMR exome

AF:

0.286

Gnomad4 ASJ exome

AF:

0.278

Gnomad4 EAS exome

AF:

0.496

Gnomad4 SAS exome

AF:

0.493

Gnomad4 FIN exome

AF:

0.363

Gnomad4 NFE exome

AF:

0.276

Gnomad4 OTH exome

AF:

0.314

GnomAD4 genome

AF:

0.324

AC:

49182

AN:

151880

Hom.:

8240

Cov.:

AF XY:

0.331

AC XY:

24575

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.363

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.263

Gnomad4 EAS

AF:

0.542

Gnomad4 SAS

AF:

0.501

Gnomad4 FIN

AF:

0.365

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.293

Alfa

AF:

0.296

Hom.:

4046

Bravo

AF:

0.315

Asia WGS

AF:

0.484

AC:

1683

AN:

3478

EpiCase

AF:

0.272

EpiControl

AF:

0.270

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Congenital microvillous atrophy

Pathogenic:1Benign:1

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Sep 05, 2021	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	May 20, 2022	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	This variant is associated with the following publications: (PMID: 24014347, 28492530, 25111220) -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

- -

Diarrhea with Microvillus Atrophy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over