Genetic Variant MYO7B:p.Tyr142Tyr (chr2-127566783-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001393586.1(MYO7B):c.426C>T(p.Tyr142Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00416 in 1,612,400 control chromosomes in the GnomAD database, including 407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0042 ( 28 hom., cov: 33)

Exomes 𝑓: 0.0042 ( 379 hom. )

Consequence

MYO7B
NM_001393586.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.113

Variant links:

Genes affected

MYO7B (HGNC:7607): (myosin VIIB) The protein encoded by this gene is found in brush border microvilli of epithelial cells in the intestines and kidneys. The encoded protein is involved in linking protocadherins to the actin cytoskeleton and is essential for proper microvilli function. This protein aids in the accumulation of intermicrovillar adhesion components such as harmonin and ANKS4B, and this accumulation is necessary for normal brush border action. [provided by RefSeq, Jan 2017]

MYO7B links:

LOC105373609 (HGNC:):

LOC105373609 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 2-127566783-C-T is Benign according to our data. Variant chr2-127566783-C-T is described in ClinVar as [Benign]. Clinvar id is 3059046.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.113 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO7B	NM_001393586.1 link	c.426C>T	p.Tyr142Tyr	synonymous_variant	Exon 5 of 48	ENST00000409816.8	NP_001380515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO7B	ENST00000409816.8 link	c.426C>T	p.Tyr142Tyr	synonymous_variant	Exon 5 of 48	1	NM_001393586.1	ENSP00000386461.3		A0A8C8KL71
MYO7B	ENST00000428314.5 link	c.426C>T	p.Tyr142Tyr	synonymous_variant	Exon 5 of 47	5		ENSP00000415090.1		Q6PIF6-1

Frequencies

GnomAD3 genomes

AF:

0.00423

AC:

644

AN:

152268

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.00310

Gnomad FIN

AF:

0.000470

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000176

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00832

AC:

2059

AN:

247524

Hom.:

107

AF XY:

0.00771

AC XY:

1036

AN XY:

134404

show subpopulations

Gnomad AFR exome

AF:

0.000904

Gnomad AMR exome

AF:

0.000377

Gnomad ASJ exome

AF:

0.000597

Gnomad EAS exome

AF:

0.104

Gnomad SAS exome

AF:

0.00284

Gnomad FIN exome

AF:

0.000696

Gnomad NFE exome

AF:

0.000204

Gnomad OTH exome

AF:

0.00498

GnomAD4 exome

AF:

0.00415

AC:

6064

AN:

1460014

Hom.:

379

Cov.:

AF XY:

0.00407

AC XY:

2953

AN XY:

726368

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.000291

Gnomad4 ASJ exome

AF:

0.000727

Gnomad4 EAS exome

AF:

0.128

Gnomad4 SAS exome

AF:

0.00285

Gnomad4 FIN exome

AF:

0.000540

Gnomad4 NFE exome

AF:

0.000134

Gnomad4 OTH exome

AF:

0.00855

GnomAD4 genome

AF:

0.00419

AC:

639

AN:

152386

Hom.:

Cov.:

AF XY:

0.00488

AC XY:

364

AN XY:

74520

show subpopulations

Gnomad4 AFR

AF:

0.00103

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.00331

Gnomad4 FIN

AF:

0.000470

Gnomad4 NFE

AF:

0.000176

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00105

Hom.:

Bravo

AF:

0.00501

Asia WGS

AF:

0.0420

AC:

146

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.000237

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MYO7B-related disorder

Benign:1

Sep 18, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

7.5

DANN

Benign

0.66

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