rs9521011

Variant summary

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

The NM_001198950.3(MYO16):​c.508-25279A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,894 control chromosomes in the GnomAD database, including 16,768 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 0.45 ( 16768 hom., cov: 32)

Consequence

MYO16
NM_001198950.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0660
Variant links:
Genes affected
MYO16 (HGNC:29822): (myosin XVI) This gene encodes an unconventional myosin protein. The encoded protein has been proposed to act as a serine/threonine phosphatase-1 targeting or regulatory subunit. Studies in a rat cell line suggest that this protein may regulate cell cycle progression. A variant within this gene may be associated with susceptibility to schizophrenia and elevated expression of this gene has been observed in the frontal cortex of human schizophrenia patients. [provided by RefSeq, Mar 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYO16NM_001198950.3 linkuse as main transcriptc.508-25279A>G intron_variant ENST00000457511.7 NP_001185879.1 F8W883

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MYO16ENST00000457511.7 linkuse as main transcriptc.508-25279A>G intron_variant 1 NM_001198950.3 ENSP00000401633.3 F8W883
MYO16ENST00000356711.7 linkuse as main transcriptc.442-25279A>G intron_variant 1 ENSP00000349145.2 Q9Y6X6-1
MYO16ENST00000251041.10 linkuse as main transcriptc.442-25279A>G intron_variant 5 ENSP00000251041.5 Q9Y6X6-3

Frequencies

GnomAD3 genomes
AF:
0.451
AC:
68388
AN:
151778
Hom.:
16754
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.241
Gnomad AMI
AF:
0.404
Gnomad AMR
AF:
0.565
Gnomad ASJ
AF:
0.403
Gnomad EAS
AF:
0.633
Gnomad SAS
AF:
0.484
Gnomad FIN
AF:
0.539
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.524
Gnomad OTH
AF:
0.484
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.450
AC:
68410
AN:
151894
Hom.:
16768
Cov.:
32
AF XY:
0.456
AC XY:
33833
AN XY:
74230
show subpopulations
Gnomad4 AFR
AF:
0.241
Gnomad4 AMR
AF:
0.566
Gnomad4 ASJ
AF:
0.403
Gnomad4 EAS
AF:
0.634
Gnomad4 SAS
AF:
0.485
Gnomad4 FIN
AF:
0.539
Gnomad4 NFE
AF:
0.524
Gnomad4 OTH
AF:
0.482
Alfa
AF:
0.488
Hom.:
3224
Bravo
AF:
0.445
Asia WGS
AF:
0.531
AC:
1843
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.9
DANN
Benign
0.47

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: rs9521011; hg19: chr13-109412704; API