Genetic Variant MYO7B:p.Leu113Leu (chr2-127566696-C-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2

The NM_001393586.1(MYO7B):c.339C>G(p.Leu113Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00237 in 1,609,518 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0019 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0024 ( 29 hom. )

Consequence

MYO7B
NM_001393586.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.277

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 2-127566696-C-G is Benign according to our data. Variant chr2-127566696-C-G is described in ClinVar as [Benign]. Clinvar id is 3038634.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.277 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 29 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO7B	NM_001393586.1 link	c.339C>G	p.Leu113Leu	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.339C>G	p.Leu113Leu	synonymous_variant	Exon 5 of 48	1	NM_001393586.1	ENSP00000386461.3		A0A8C8KL71
MYO7B	ENST00000428314.5 link	c.339C>G	p.Leu113Leu	synonymous_variant	Exon 5 of 47	5		ENSP00000415090.1		Q6PIF6-1

Frequencies

GnomAD3 genomes

AF:

0.00195

AC:

297

AN:

152258

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00432

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0159

Gnomad FIN

AF:

0.000564

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00181

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00339

AC:

818

AN:

241146

Hom.:

AF XY:

0.00415

AC XY:

543

AN XY:

130998

show subpopulations

Gnomad AFR exome

AF:

0.000404

Gnomad AMR exome

AF:

0.00139

Gnomad ASJ exome

AF:

0.00222

Gnomad EAS exome

AF:

0.0000571

Gnomad SAS exome

AF:

0.0161

Gnomad FIN exome

AF:

0.000708

Gnomad NFE exome

AF:

0.00212

Gnomad OTH exome

AF:

0.00255

GnomAD4 exome

AF:

0.00242

AC:

3525

AN:

1457142

Hom.:

Cov.:

AF XY:

0.00288

AC XY:

2084

AN XY:

724700

show subpopulations

Gnomad4 AFR exome

AF:

0.000269

Gnomad4 AMR exome

AF:

0.00145

Gnomad4 ASJ exome

AF:

0.00227

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.0156

Gnomad4 FIN exome

AF:

0.000424

Gnomad4 NFE exome

AF:

0.00166

Gnomad4 OTH exome

AF:

0.00244

GnomAD4 genome

AF:

0.00193

AC:

294

AN:

152376

Hom.:

Cov.:

AF XY:

0.00224

AC XY:

167

AN XY:

74514

show subpopulations

Gnomad4 AFR

AF:

0.000240

Gnomad4 AMR

AF:

0.00431

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0153

Gnomad4 FIN

AF:

0.000564

Gnomad4 NFE

AF:

0.00181

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00138

Hom.:

Bravo

AF:

0.00181

Asia WGS

AF:

0.00693

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MYO7B-related disorder

Benign:1

Mar 25, 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

-0.49

CADD

Benign

3.7

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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