rs2032487

chr22-36299382-C-T

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.2977-340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,136 control chromosomes in the GnomAD database, including 52,738 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.79 (52738 hom., cov: 32)
• Consequence: MYH9 NM_002473.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.42

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=-0.91).
• BP6: Variant 22-36299382-C-T is Benign according to our data. Variant chr22-36299382-C-T is described in ClinVar as [Benign]. Clinvar id is 1244672.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH9	NM_002473.6	c.2977-340G>A		intron_variant		ENST00000216181.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH9	ENST00000216181.11	c.2977-340G>A		intron_variant		1	NM_002473.6	P1
MYH9	ENST00000685801.1	c.3040-340G>A		intron_variant
MYH9	ENST00000691109.1	n.3272-340G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120233 AN: 152018 Hom.: 52725 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.791 AC: 120284 AN: 152136 Hom.: 52738 Cov.: 32 AF XY: 0.796 AC XY: 59206 AN XY: 74378

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.845

Alfa AF: 0.930 Hom.: 73188

Bravo AF: 0.769

Asia WGS AF: 0.943 AC: 3279 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	-0.91
Cadd	Benign	0.036
Dann	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2032487; hg19: chr22-36695428;