Variant rs883223 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_000260.4(MYO7A):c.6439-31G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,613,084 control chromosomes in the GnomAD database, including 101,895 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 9461 hom., cov: 34)

Exomes 𝑓: 0.35 ( 92434 hom. )

Consequence

MYO7A
NM_000260.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0460

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 11-77213829-G-A is Benign according to our data. Variant chr11-77213829-G-A is described in ClinVar as [Benign]. Clinvar id is 255666.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-77213829-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO7A	NM_000260.4 linkuse as main transcript	c.6439-31G>A		intron_variant		ENST00000409709.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO7A	ENST00000409709.9 linkuse as main transcript	c.6439-31G>A		intron_variant		1	NM_000260.4		Q13402-1

Frequencies

GnomAD3 genomes

AF:

0.347

AC:

52823

AN:

152052

Hom.:

9451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.466

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.468

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.346

GnomAD3 exomes

AF:

0.383

AC:

95239

AN:

248736

Hom.:

19343

AF XY:

0.374

AC XY:

50449

AN XY:

134944

show subpopulations

Gnomad AFR exome

AF:

0.302

Gnomad AMR exome

AF:

0.571

Gnomad ASJ exome

AF:

0.352

Gnomad EAS exome

AF:

0.486

Gnomad SAS exome

AF:

0.371

Gnomad FIN exome

AF:

0.327

Gnomad NFE exome

AF:

0.338

Gnomad OTH exome

AF:

0.361

GnomAD4 exome

AF:

0.352

AC:

513534

AN:

1460916

Hom.:

92434

Cov.:

AF XY:

0.351

AC XY:

255085

AN XY:

726736

show subpopulations

Gnomad4 AFR exome

AF:

0.308

Gnomad4 AMR exome

AF:

0.561

Gnomad4 ASJ exome

AF:

0.351

Gnomad4 EAS exome

AF:

0.502

Gnomad4 SAS exome

AF:

0.373

Gnomad4 FIN exome

AF:

0.337

Gnomad4 NFE exome

AF:

0.338

Gnomad4 OTH exome

AF:

0.354

GnomAD4 genome

AF:

0.347

AC:

52861

AN:

152168

Hom.:

9461

Cov.:

AF XY:

0.348

AC XY:

25856

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.308

Gnomad4 AMR

AF:

0.467

Gnomad4 ASJ

AF:

0.356

Gnomad4 EAS

AF:

0.469

Gnomad4 SAS

AF:

0.364

Gnomad4 FIN

AF:

0.321

Gnomad4 NFE

AF:

0.336

Gnomad4 OTH

AF:

0.345

Alfa

AF:

0.344

Hom.:

8677

Bravo

AF:

0.359

Asia WGS

AF:

0.388

AC:

1349

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

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

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 24, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.3

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