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rs9634572

Variant summary

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

The NM_001198950.3(MYO16):c.508-11789C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,096 control chromosomes in the GnomAD database, including 2,839 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 0.18 ( 2839 hom., cov: 33)

Consequence

MYO16
NM_001198950.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.360
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]

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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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYO16NM_001198950.3 linkuse as main transcriptc.508-11789C>A intron_variant ENST00000457511.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYO16ENST00000457511.7 linkuse as main transcriptc.508-11789C>A intron_variant 1 NM_001198950.3 A2
MYO16ENST00000356711.7 linkuse as main transcriptc.442-11789C>A intron_variant 1 P2Q9Y6X6-1
MYO16ENST00000251041.10 linkuse as main transcriptc.442-11789C>A intron_variant 5 Q9Y6X6-3

Frequencies

GnomAD3 genomes
AF:
0.182
AC:
27655
AN:
151978
Hom.:
2827
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.280
Gnomad AMI
AF:
0.0989
Gnomad AMR
AF:
0.147
Gnomad ASJ
AF:
0.142
Gnomad EAS
AF:
0.244
Gnomad SAS
AF:
0.180
Gnomad FIN
AF:
0.0722
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.147
Gnomad OTH
AF:
0.164
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.182
AC:
27681
AN:
152096
Hom.:
2839
Cov.:
33
AF XY:
0.178
AC XY:
13207
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.280
Gnomad4 AMR
AF:
0.146
Gnomad4 ASJ
AF:
0.142
Gnomad4 EAS
AF:
0.244
Gnomad4 SAS
AF:
0.179
Gnomad4 FIN
AF:
0.0722
Gnomad4 NFE
AF:
0.147
Gnomad4 OTH
AF:
0.164
Alfa
AF:
0.155
Hom.:
362
Bravo
AF:
0.187
Asia WGS
AF:
0.217
AC:
756
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
Cadd
Benign
3.3
Dann
Benign
0.42

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: rs9634572; hg19: chr13-109426194; API