rs2071733

chr22-36284779-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_002473.6(MYH9):c.5484-268G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,028 control chromosomes in the GnomAD database, including 39,361 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.71 (39361 hom., cov: 31)
• Consequence: MYH9 NM_002473.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.575

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 22-36284779-C-G is Benign according to our data. Variant chr22-36284779-C-G is described in ClinVar as [Benign]. Clinvar id is 1276096.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH9	NM_002473.6	c.5484-268G>C		intron_variant		ENST00000216181.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH9	ENST00000216181.11	c.5484-268G>C		intron_variant		1	NM_002473.6	P1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107689 AN: 151910 Hom.: 39309 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.709 AC: 107783 AN: 152028 Hom.: 39361 Cov.: 31 AF XY: 0.706 AC XY: 52408 AN XY: 74284

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.651

Alfa AF: 0.706 Hom.: 4768

Bravo AF: 0.712

Asia WGS AF: 0.424 AC: 1479 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.24
Dann	Benign	0.41

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

Other links and lift over

dbSNP: rs2071733; hg19: chr22-36680825;