rs9514923

Positions:

• chr13-108814281-A-G
• chr13-108814281-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001198950.3(MYO16):​c.868-6056A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,152 control chromosomes in the GnomAD database, including 59,495 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 0.86 (59495 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO16	NM_001198950.3	c.868-6056A>G		intron_variant		ENST00000457511.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO16	ENST00000457511.7	c.868-6056A>G		intron_variant		1	NM_001198950.3	A2
MYO16	ENST00000356711.7	c.802-6056A>G		intron_variant		1		P2
MYO16	ENST00000251041.10	c.802-6056A>G		intron_variant		5
MYO16	ENST00000375857.6	n.188-6056A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130588 AN: 152034 Hom.: 59486 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.893

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.859 AC: 130631 AN: 152152 Hom.: 59495 Cov.: 32 AF XY: 0.862 AC XY: 64156 AN XY: 74406

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.976

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.997

Gnomad4 OTH AF: 0.893

Alfa AF: 0.917 Hom.: 7800

Bravo AF: 0.839

Asia WGS AF: 0.941 AC: 3265 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.013
DANN	Benign	0.45

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

Other links and lift over

dbSNP: rs9514923; hg19: chr13-109466629;