rs1320702

Variant names:

• chr11-77208820-T-A
• rs1320702
• NM_000260.4:c.6051+17T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-77208820-T-A
• chr11-77208820-T-G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000260.4(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 NM_000260.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:9
• Conservation: PhyloP100: -0.927
• Publications: 14 publications found

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 Gene-Disease associations (from GenCC):

• nonsyndromic genetic hearing loss

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• autosomal recessive nonsyndromic hearing loss 2

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, G2P
• Usher syndrome type 1

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, PanelApp Australia
• Usher syndrome type 1B

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• autosomal dominant nonsyndromic hearing loss 11

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, PanelApp Australia, Labcorp Genetics (formerly Invitae)
• autosomal dominant nonsyndromic hearing loss

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hearing loss, autosomal recessive

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Usher syndrome type 2

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 VariationId is 43315.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• 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 rank	MANE	Protein	UniProt
MYO7A	NM_000260.4	c.6051+17T>A		intron_variant	Intron 44 of 48	ENST00000409709.9	NP_000251.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO7A	ENST00000409709.9	c.6051+17T>A		intron_variant	Intron 44 of 48	1	NM_000260.4	ENSP00000386331.3
MYO7A	ENST00000458637.6	c.5937+17T>A		intron_variant	Intron 44 of 48	1		ENSP00000392185.2
MYO7A	ENST00000409619.6	c.5904+17T>A		intron_variant	Intron 45 of 49	1		ENSP00000386635.2
MYO7A	ENST00000458169.2	c.3477+17T>A		intron_variant	Intron 24 of 28	1		ENSP00000417017.2
MYO7A	ENST00000670577.1	n.*623+17T>A		intron_variant	Intron 27 of 31			ENSP00000499323.1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85319 AN: 152036 Hom.: 24143 Cov.: 33

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

GnomAD2 exomes AF: 0.566 AC: 90943 AN: 160660 AF XY: 0.556

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 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.: 27 AF XY: 0.558 AC XY: 377451 AN XY: 676020

African (AFR) AF: 0.520 AC: 16090 AN: 30936

American (AMR) AF: 0.664 AC: 23872 AN: 35930

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 13026 AN: 24988

East Asian (EAS) AF: 0.480 AC: 17136 AN: 35716

South Asian (SAS) AF: 0.432 AC: 33940 AN: 78584

European-Finnish (FIN) AF: 0.652 AC: 31487 AN: 48266

Middle Eastern (MID) AF: 0.583 AC: 3289 AN: 5646

European-Non Finnish (NFE) AF: 0.570 AC: 597155 AN: 1048518

Other (OTH) AF: 0.552 AC: 31492 AN: 57068

GnomAD4 genome AF: 0.561 AC: 85420 AN: 152154 Hom.: 24181 Cov.: 33 AF XY: 0.563 AC XY: 41898 AN XY: 74388

African (AFR) AF: 0.526 AC: 21815 AN: 41496

American (AMR) AF: 0.621 AC: 9505 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1832 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2508 AN: 5176

South Asian (SAS) AF: 0.415 AC: 1999 AN: 4822

European-Finnish (FIN) AF: 0.653 AC: 6924 AN: 10602

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38883 AN: 67976

Other (OTH) AF: 0.579 AC: 1222 AN: 2112

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:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:3

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 23, 2009

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 22, 2025

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:3

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Autosomal recessive nonsyndromic hearing loss 2 Benign:1

Jul 01, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal dominant nonsyndromic hearing loss 11 Benign:1

Jul 01, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Usher syndrome type 1 Benign:1

Jul 01, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.10
DANN	Benign	0.61
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1320702; hg19: chr11-76919865; COSMIC: COSV68686298; COSMIC: COSV68686298;