rs726449

Positions:

• chr13-108499141-C-T

Variant summary

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

The XM_011521062.2(MYO16):​c.-39+3217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,148 control chromosomes in the GnomAD database, including 6,320 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 0.28 (6320 hom., cov: 33)
• Consequence: MYO16 XM_011521062.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO16	XM_011521062.2	c.-39+3217C>T		intron_variant			XP_011519364.1
MYO16	XM_047430183.1	c.-39+3217C>T		intron_variant			XP_047286139.1
		n.108499141C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42087 AN: 152030 Hom.: 6322 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.277 AC: 42085 AN: 152148 Hom.: 6320 Cov.: 33 AF XY: 0.271 AC XY: 20135 AN XY: 74368

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.273

Alfa AF: 0.314 Hom.: 3956

Bravo AF: 0.275

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs726449; hg19: chr13-109151489;