ENST00000216181:c.*1160dupT

Variant names:

• chr22-36281507-T-TA
• rs56058205
• ENST00000216181:c.*1160dupT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000216181(MYH9):​c.*1160dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00807 in 205,504 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0012 (1 hom., cov: 29)
  • Exomes 𝑓: 0.026 (1 hom.)
• Consequence: MYH9 ENST00000216181 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00118 (175/147772) while in subpopulation EAS AF= 0.00693 (35/5054). AF 95% confidence interval is 0.00512. There are 1 homozygotes in gnomad4. There are 85 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 175 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH9	NM_002473.6	c.*1160dupT		3_prime_UTR_variant	Exon 41 of 41	ENST00000216181.11	NP_002464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH9	ENST00000216181	c.*1160dupT		3_prime_UTR_variant	Exon 41 of 41	1	NM_002473.6	ENSP00000216181.6

Frequencies

GnomAD3 genomes AF: 0.00118 AC: 174 AN: 147706 Hom.: 1 Cov.: 29

Gnomad AFR AF: 0.000665

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00182

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00691

Gnomad SAS AF: 0.00149

Gnomad FIN AF: 0.000320

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00111

Gnomad OTH AF: 0.000498

GnomAD4 exome AF: 0.0257 AC: 1484 AN: 57732 Hom.: 1 Cov.: 0 AF XY: 0.0253 AC XY: 675 AN XY: 26678

Gnomad4 AFR exome AF: 0.0160

Gnomad4 AMR exome AF: 0.0293

Gnomad4 ASJ exome AF: 0.0166

Gnomad4 EAS exome AF: 0.0526

Gnomad4 SAS exome AF: 0.0255

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0223

Gnomad4 OTH exome AF: 0.0210

GnomAD4 genome AF: 0.00118 AC: 175 AN: 147772 Hom.: 1 Cov.: 29 AF XY: 0.00118 AC XY: 85 AN XY: 71914

Gnomad4 AFR AF: 0.000688

Gnomad4 AMR AF: 0.00182

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00693

Gnomad4 SAS AF: 0.00150

Gnomad4 FIN AF: 0.000320

Gnomad4 NFE AF: 0.00111

Gnomad4 OTH AF: 0.000494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs56058205; hg19: chr22-36677553;