Variant 22-36312004-CTCCTGTGA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_002473.6(MYH9):c.1728+37_1728+44del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 1,611,926 control chromosomes in the GnomAD database, including 50,136 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3998 hom., cov: 26)

Exomes 𝑓: 0.23 ( 46138 hom. )

Consequence

MYH9
NM_002473.6 intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: -0.178

Variant links:

Genes affected

MYH9 (HGNC:7579): (myosin heavy chain 9) This gene encodes a conventional non-muscle myosin; this protein should not be confused with the unconventional myosin-9a or 9b (MYO9A or MYO9B). The encoded protein is a myosin IIA heavy chain that contains an IQ domain and a myosin head-like domain which is involved in several important functions, including cytokinesis, cell motility and maintenance of cell shape. Defects in this gene have been associated with non-syndromic sensorineural deafness autosomal dominant type 17, Epstein syndrome, Alport syndrome with macrothrombocytopenia, Sebastian syndrome, Fechtner syndrome and macrothrombocytopenia with progressive sensorineural deafness. [provided by RefSeq, Dec 2011]

MYH9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 22-36312004-CTCCTGTGA-C is Benign according to our data. Variant chr22-36312004-CTCCTGTGA-C is described in ClinVar as [Benign]. Clinvar id is 258730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYH9	NM_002473.6 linkuse as main transcript	c.1728+37_1728+44del		intron_variant		ENST00000216181.11	NP_002464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYH9	ENST00000216181.11 linkuse as main transcript	c.1728+37_1728+44del		intron_variant		1	NM_002473.6	ENSP00000216181	P1	P35579-1

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

30409

AN:

151968

Hom.:

3985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0820

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.624

Gnomad SAS

AF:

0.447

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.230

GnomAD3 exomes

AF:

0.272

AC:

68335

AN:

251072

Hom.:

11623

AF XY:

0.280

AC XY:

38077

AN XY:

135754

show subpopulations

Gnomad AFR exome

AF:

0.0767

Gnomad AMR exome

AF:

0.291

Gnomad ASJ exome

AF:

0.351

Gnomad EAS exome

AF:

0.621

Gnomad SAS exome

AF:

0.434

Gnomad FIN exome

AF:

0.196

Gnomad NFE exome

AF:

0.203

Gnomad OTH exome

AF:

0.252

GnomAD4 exome

AF:

0.232

AC:

338216

AN:

1459838

Hom.:

46138

AF XY:

0.238

AC XY:

172938

AN XY:

726222

show subpopulations

Gnomad4 AFR exome

AF:

0.0764

Gnomad4 AMR exome

AF:

0.286

Gnomad4 ASJ exome

AF:

0.353

Gnomad4 EAS exome

AF:

0.623

Gnomad4 SAS exome

AF:

0.430

Gnomad4 FIN exome

AF:

0.195

Gnomad4 NFE exome

AF:

0.202

Gnomad4 OTH exome

AF:

0.257

GnomAD4 genome

AF:

0.200

AC:

30445

AN:

152088

Hom.:

3998

Cov.:

AF XY:

0.208

AC XY:

15459

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.0820

Gnomad4 AMR

AF:

0.257

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.625

Gnomad4 SAS

AF:

0.446

Gnomad4 FIN

AF:

0.193

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.235

Alfa

AF:

0.215

Hom.:

680

Bravo

AF:

0.198

Asia WGS

AF:

0.522

AC:

1814

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Jul 15, 2024	This variant is classified as Benign based on local population frequency. This variant was detected in 32% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 30. Only high quality variants are reported. -

Autosomal dominant nonsyndromic hearing loss 17

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 16, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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