rs9521010

Positions:

• chr13-108760291-G-A
• chr13-108760291-G-T

Variant summary

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

The NM_001198950.3(MYO16):​c.508-25344G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,842 control chromosomes in the GnomAD database, including 16,556 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 (16556 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO16	NM_001198950.3	c.508-25344G>A		intron_variant		ENST00000457511.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO16	ENST00000457511.7	c.508-25344G>A		intron_variant		1	NM_001198950.3	A2
MYO16	ENST00000356711.7	c.442-25344G>A		intron_variant		1		P2
MYO16	ENST00000251041.10	c.442-25344G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67986 AN: 151724 Hom.: 16542 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.448 AC: 68009 AN: 151842 Hom.: 16556 Cov.: 32 AF XY: 0.453 AC XY: 33591 AN XY: 74192

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.479

Alfa AF: 0.513 Hom.: 31311

Bravo AF: 0.441

Asia WGS AF: 0.531 AC: 1841 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.22

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: rs9521010; hg19: chr13-109412639;