chr22-36322414-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_002473.6(MYH9):c.705+15G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,613,438 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00011 ( 0 hom. )

Consequence

MYH9
NM_002473.6 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -3.49

Publications

0 publications found

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 Gene-Disease associations (from GenCC):

autosomal dominant nonsyndromic hearing loss 17
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen
May-Hegglin anomaly
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
autosomal dominant nonsyndromic hearing loss
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

MYH9 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 22-36322414-C-T is Benign according to our data. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36322414-C-T is described in CliVar as Likely_benign. Clinvar id is 258764.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.000158 (24/152264) while in subpopulation AMR AF = 0.000262 (4/15290). AF 95% confidence interval is 0.000102. There are 0 homozygotes in GnomAd4. There are 8 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High AC in GnomAd4 at 24 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH9	NM_002473.6 link	c.705+15G>A		intron_variant	Intron 6 of 40	ENST00000216181.11	NP_002464.1	P35579-1A0A024R1N1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH9	ENST00000216181.11 link	c.705+15G>A		intron_variant	Intron 6 of 40	1	NM_002473.6	ENSP00000216181.6		P35579-1

Frequencies

GnomAD3 genomes

AF:

0.000158

AC:

AN:

152264

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000176

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000797

AC:

AN:

250852

AF XY:

0.0000589

show subpopulations

Gnomad AFR exome

AF:

0.000310

Gnomad AMR exome

AF:

0.0000868

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000882

Gnomad OTH exome

AF:

0.000326

GnomAD4 exome

AF:

0.000114

AC:

166

AN:

1461174

Hom.:

Cov.:

AF XY:

0.0000990

AC XY:

AN XY:

726956

show subpopulations

African (AFR)

AF:

0.0000299

AC:

AN:

33468

American (AMR)

AF:

0.0000895

AC:

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26122

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39694

South Asian (SAS)

AF:

0.00

AC:

AN:

86246

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53104

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.000135

AC:

150

AN:

1111674

Other (OTH)

AF:

0.000166

AC:

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000158

AC:

AN:

152264

Hom.:

Cov.:

AF XY:

0.000108

AC XY:

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.000193

AC:

AN:

41480

American (AMR)

AF:

0.000262

AC:

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5194

South Asian (SAS)

AF:

0.00

AC:

AN:

4838

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.000176

AC:

AN:

68044

Other (OTH)

AF:

0.00

AC:

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.527

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000868

Hom.:

Bravo

AF:

0.000223

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Autosomal dominant nonsyndromic hearing loss 17;C5200934:Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

Benign:1

Apr 27, 2022

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Jan 14, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely 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

-0.82

CADD

Benign

0.11

(source)

DANN

Benign

0.60

PhyloP100

-3.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over