rs7321660

Positions:

• chr13-108871564-T-C

Variant summary

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

The NM_001198950.3(MYO16):​c.1425+5322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,986 control chromosomes in the GnomAD database, including 8,000 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 0.32 (8000 hom., cov: 31)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

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 = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO16	NM_001198950.3	c.1425+5322T>C		intron_variant		ENST00000457511.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO16	ENST00000457511.7	c.1425+5322T>C		intron_variant		1	NM_001198950.3	A2

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47880 AN: 151866 Hom.: 7989 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.315 AC: 47924 AN: 151986 Hom.: 8000 Cov.: 31 AF XY: 0.306 AC XY: 22743 AN XY: 74302

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0149

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.323

Alfa AF: 0.348 Hom.: 5180

Bravo AF: 0.315

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.38

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: rs7321660; hg19: chr13-109523912;