rs4820234

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000216181.11(MYH9):​c.491-5541T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,982 control chromosomes in the GnomAD database, including 29,224 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 29224 hom., cov: 31)

Consequence

MYH9
ENST00000216181.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.276
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYH9NM_002473.6 linkuse as main transcriptc.491-5541T>C intron_variant ENST00000216181.11 NP_002464.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MYH9ENST00000216181.11 linkuse as main transcriptc.491-5541T>C intron_variant 1 NM_002473.6 ENSP00000216181 P1P35579-1

Frequencies

GnomAD3 genomes
AF:
0.610
AC:
92651
AN:
151864
Hom.:
29196
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.702
Gnomad AMI
AF:
0.685
Gnomad AMR
AF:
0.628
Gnomad ASJ
AF:
0.482
Gnomad EAS
AF:
0.162
Gnomad SAS
AF:
0.397
Gnomad FIN
AF:
0.617
Gnomad MID
AF:
0.623
Gnomad NFE
AF:
0.605
Gnomad OTH
AF:
0.589
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.610
AC:
92719
AN:
151982
Hom.:
29224
Cov.:
31
AF XY:
0.606
AC XY:
44989
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.702
Gnomad4 AMR
AF:
0.627
Gnomad4 ASJ
AF:
0.482
Gnomad4 EAS
AF:
0.161
Gnomad4 SAS
AF:
0.397
Gnomad4 FIN
AF:
0.617
Gnomad4 NFE
AF:
0.605
Gnomad4 OTH
AF:
0.583
Alfa
AF:
0.598
Hom.:
12592
Bravo
AF:
0.617
Asia WGS
AF:
0.294
AC:
1025
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.2
DANN
Benign
0.27

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4820234; hg19: chr22-36729074; API