rs9514918

Variant summary

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

The ENST00000457511.7(MYO16):​c.742-1810G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,126 control chromosomes in the GnomAD database, including 41,054 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 0.72 ( 41054 hom., cov: 32)

Consequence

MYO16
ENST00000457511.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470
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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYO16NM_001198950.3 linkuse as main transcriptc.742-1810G>C intron_variant ENST00000457511.7 NP_001185879.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MYO16ENST00000457511.7 linkuse as main transcriptc.742-1810G>C intron_variant 1 NM_001198950.3 ENSP00000401633 A2
MYO16ENST00000356711.7 linkuse as main transcriptc.676-1810G>C intron_variant 1 ENSP00000349145 P2Q9Y6X6-1
MYO16ENST00000251041.10 linkuse as main transcriptc.676-1810G>C intron_variant 5 ENSP00000251041 Q9Y6X6-3
MYO16ENST00000375857.6 linkuse as main transcriptn.62-1810G>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.723
AC:
109914
AN:
152008
Hom.:
41020
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.531
Gnomad AMI
AF:
0.884
Gnomad AMR
AF:
0.802
Gnomad ASJ
AF:
0.845
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.880
Gnomad FIN
AF:
0.833
Gnomad MID
AF:
0.820
Gnomad NFE
AF:
0.763
Gnomad OTH
AF:
0.745
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.723
AC:
110000
AN:
152126
Hom.:
41054
Cov.:
32
AF XY:
0.731
AC XY:
54368
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.531
Gnomad4 AMR
AF:
0.803
Gnomad4 ASJ
AF:
0.845
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.881
Gnomad4 FIN
AF:
0.833
Gnomad4 NFE
AF:
0.763
Gnomad4 OTH
AF:
0.748
Alfa
AF:
0.691
Hom.:
2213
Bravo
AF:
0.712
Asia WGS
AF:
0.912
AC:
3171
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.7
DANN
Benign
0.36

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: rs9514918; hg19: chr13-109457217; API