Variant rs1320702 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 ENST00000409709.9(MYO7A):c.6051+17T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 1,517,806 control chromosomes in the GnomAD database, including 242,007 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 24181 hom., cov: 33)

Exomes 𝑓: 0.56 ( 217826 hom. )

Consequence

MYO7A
ENST00000409709.9 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.927

Variant links:

Genes affected

MYO7A (HGNC:7606): (myosin VIIA) This gene is a member of the myosin gene family. Myosins are mechanochemical proteins characterized by the presence of a motor domain, an actin-binding domain, a neck domain that interacts with other proteins, and a tail domain that serves as an anchor. This gene encodes an unconventional myosin with a very short tail. Defects in this gene are associated with the mouse shaker-1 phenotype and the human Usher syndrome 1B which are characterized by deafness, reduced vestibular function, and (in human) retinal degeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

MYO7A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 11-77208820-T-A is Benign according to our data. Variant chr11-77208820-T-A is described in ClinVar as [Benign]. Clinvar id is 43315.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-77208820-T-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO7A	NM_000260.4 linkuse as main transcript	c.6051+17T>A		intron_variant		ENST00000409709.9	NP_000251.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO7A	ENST00000409709.9 linkuse as main transcript	c.6051+17T>A		intron_variant		1	NM_000260.4	ENSP00000386331		Q13402-1

Frequencies

GnomAD3 genomes

AF:

0.561

AC:

85319

AN:

152036

Hom.:

24143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.525

Gnomad AMI

AF:

0.604

Gnomad AMR

AF:

0.621

Gnomad ASJ

AF:

0.528

Gnomad EAS

AF:

0.484

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.653

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.572

Gnomad OTH

AF:

0.580

GnomAD3 exomes

AF:

0.566

AC:

90943

AN:

160660

Hom.:

26312

AF XY:

0.556

AC XY:

47238

AN XY:

84982

show subpopulations

Gnomad AFR exome

AF:

0.518

Gnomad AMR exome

AF:

0.670

Gnomad ASJ exome

AF:

0.525

Gnomad EAS exome

AF:

0.506

Gnomad SAS exome

AF:

0.429

Gnomad FIN exome

AF:

0.656

Gnomad NFE exome

AF:

0.575

Gnomad OTH exome

AF:

0.558

GnomAD4 exome

AF:

0.562

AC:

767487

AN:

1365652

Hom.:

217826

Cov.:

AF XY:

0.558

AC XY:

377451

AN XY:

676020

show subpopulations

Gnomad4 AFR exome

AF:

0.520

Gnomad4 AMR exome

AF:

0.664

Gnomad4 ASJ exome

AF:

0.521

Gnomad4 EAS exome

AF:

0.480

Gnomad4 SAS exome

AF:

0.432

Gnomad4 FIN exome

AF:

0.652

Gnomad4 NFE exome

AF:

0.570

Gnomad4 OTH exome

AF:

0.552

GnomAD4 genome

AF:

0.561

AC:

85420

AN:

152154

Hom.:

24181

Cov.:

AF XY:

0.563

AC XY:

41898

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.526

Gnomad4 AMR

AF:

0.621

Gnomad4 ASJ

AF:

0.528

Gnomad4 EAS

AF:

0.485

Gnomad4 SAS

AF:

0.415

Gnomad4 FIN

AF:

0.653

Gnomad4 NFE

AF:

0.572

Gnomad4 OTH

AF:

0.579

Alfa

AF:

0.502

Hom.:

2667

Bravo

AF:

0.561

Asia WGS

AF:

0.445

AC:

1548

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 23, 2009	- -

Autosomal recessive nonsyndromic hearing loss 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Autosomal dominant nonsyndromic hearing loss 11

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Usher syndrome type 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.10

DANN

Benign

0.61

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