22-36331506-G-T

Variant summary

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

The NM_002473.6(MYH9):​c.491-4018C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,982 control chromosomes in the GnomAD database, including 19,595 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 0.48 ( 19595 hom., cov: 32)

Consequence

MYH9
NM_002473.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.521
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=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYH9NM_002473.6 linkuse as main transcriptc.491-4018C>A intron_variant ENST00000216181.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYH9ENST00000216181.11 linkuse as main transcriptc.491-4018C>A intron_variant 1 NM_002473.6 P1P35579-1

Frequencies

GnomAD3 genomes
AF:
0.481
AC:
73109
AN:
151862
Hom.:
19595
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.267
Gnomad AMI
AF:
0.686
Gnomad AMR
AF:
0.581
Gnomad ASJ
AF:
0.478
Gnomad EAS
AF:
0.158
Gnomad SAS
AF:
0.376
Gnomad FIN
AF:
0.608
Gnomad MID
AF:
0.601
Gnomad NFE
AF:
0.598
Gnomad OTH
AF:
0.506
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.481
AC:
73117
AN:
151982
Hom.:
19595
Cov.:
32
AF XY:
0.480
AC XY:
35642
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.267
Gnomad4 AMR
AF:
0.580
Gnomad4 ASJ
AF:
0.478
Gnomad4 EAS
AF:
0.158
Gnomad4 SAS
AF:
0.377
Gnomad4 FIN
AF:
0.608
Gnomad4 NFE
AF:
0.598
Gnomad4 OTH
AF:
0.501
Alfa
AF:
0.568
Hom.:
27479
Bravo
AF:
0.470
Asia WGS
AF:
0.251
AC:
876
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
7.6
DANN
Benign
0.87

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

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

Other links and lift over

dbSNP: rs8143119; hg19: chr22-36727551; API