rs9521011

Positions:

• chr13-108760356-A-G
• chr13-108760356-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.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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

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=-0.87).
• 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
MYO16	NM_001198950.3	c.508-25279A>G		intron_variant		ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000457511.7	c.508-25279A>G		intron_variant		1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.442-25279A>G		intron_variant		1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.442-25279A>G		intron_variant		5		ENSP00000251041.5

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68388 AN: 151778 Hom.: 16754 Cov.: 32

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

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

Other links and lift over

dbSNP: rs9521011; hg19: chr13-109412704;