Variant chr15-59137366-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004998.4(MYO1E):c.*14C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 1,613,270 control chromosomes in the GnomAD database, including 496 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.034 ( 169 hom., cov: 32)

Exomes 𝑓: 0.011 ( 327 hom. )

Consequence

MYO1E
NM_004998.4 3_prime_UTR

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.188

Variant links:

Genes affected

MYO1E (HGNC:7599): (myosin IE) This gene encodes a member of the nonmuscle class I myosins which are a subgroup of the unconventional myosin protein family. The unconventional myosin proteins function as actin-based molecular motors. Class I myosins are characterized by a head (motor) domain, a regulatory domain and a either a short or long tail domain. Among the class I myosins, this protein is distinguished by a long tail domain that is involved in crosslinking actin filaments. This protein localizes to the cytoplasm and may be involved in intracellular movement and membrane trafficking. Mutations in this gene are the cause of focal segmental glomerulosclerosis-6. This gene has been referred to as myosin IC in the literature but is distinct from the myosin IC gene located on chromosome 17. [provided by RefSeq, Jan 2012]

MYO1E links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 15-59137366-G-C is Benign according to our data. Variant chr15-59137366-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1294548.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-59137366-G-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.082 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO1E	NM_004998.4 linkuse as main transcript	c.*14C>G		3_prime_UTR_variant	28/28	ENST00000288235.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO1E	ENST00000288235.9 linkuse as main transcript	c.*14C>G		3_prime_UTR_variant	28/28	1	NM_004998.4	P1
MYO1E	ENST00000559412.1 linkuse as main transcript	c.130-589C>G		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0342

AC:

5203

AN:

152160

Hom.:

167

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0841

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0169

Gnomad ASJ

AF:

0.0343

Gnomad EAS

AF:

0.0380

Gnomad SAS

AF:

0.0155

Gnomad FIN

AF:

0.0532

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.00635

Gnomad OTH

AF:

0.0263

GnomAD3 exomes

AF:

0.0215

AC:

5396

AN:

251350

Hom.:

123

AF XY:

0.0194

AC XY:

2642

AN XY:

135848

show subpopulations

Gnomad AFR exome

AF:

0.0831

Gnomad AMR exome

AF:

0.0190

Gnomad ASJ exome

AF:

0.0339

Gnomad EAS exome

AF:

0.0308

Gnomad SAS exome

AF:

0.0133

Gnomad FIN exome

AF:

0.0518

Gnomad NFE exome

AF:

0.00753

Gnomad OTH exome

AF:

0.0156

GnomAD4 exome

AF:

0.0114

AC:

16646

AN:

1460992

Hom.:

327

Cov.:

AF XY:

0.0111

AC XY:

8040

AN XY:

726878

show subpopulations

Gnomad4 AFR exome

AF:

0.0873

Gnomad4 AMR exome

AF:

0.0196

Gnomad4 ASJ exome

AF:

0.0357

Gnomad4 EAS exome

AF:

0.0457

Gnomad4 SAS exome

AF:

0.0128

Gnomad4 FIN exome

AF:

0.0526

Gnomad4 NFE exome

AF:

0.00454

Gnomad4 OTH exome

AF:

0.0170

GnomAD4 genome

AF:

0.0343

AC:

5216

AN:

152278

Hom.:

169

Cov.:

AF XY:

0.0361

AC XY:

2686

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0843

Gnomad4 AMR

AF:

0.0169

Gnomad4 ASJ

AF:

0.0343

Gnomad4 EAS

AF:

0.0377

Gnomad4 SAS

AF:

0.0151

Gnomad4 FIN

AF:

0.0532

Gnomad4 NFE

AF:

0.00635

Gnomad4 OTH

AF:

0.0260

Alfa

AF:

0.0221

Hom.:

Bravo

AF:

0.0335

Asia WGS

AF:

0.0390

AC:

135

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 15, 2020	- -

Kidney disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Feb 06, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.8

DANN

Benign

0.53

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.

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