13-108724645-C-T

Variant names:

• chr13-108724645-C-T
• rs9520990
• NM_001198950.3:c.364-2795C>T

Variant summary

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

The NM_001198950.3(MYO16):​c.364-2795C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,798 control chromosomes in the GnomAD database, including 5,155 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 0.23 (5155 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.693

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO16	NM_001198950.3	c.364-2795C>T		intron_variant	Intron 3 of 34	ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000457511.7	c.364-2795C>T		intron_variant	Intron 3 of 34	1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.298-2795C>T		intron_variant	Intron 3 of 34	1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.298-2795C>T		intron_variant	Intron 3 of 24	5		ENSP00000251041.5

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35633 AN: 151680 Hom.: 5146 Cov.: 32

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.235 AC: 35645 AN: 151798 Hom.: 5155 Cov.: 32 AF XY: 0.245 AC XY: 18198 AN XY: 74142

Gnomad4 AFR AF: 0.0893

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.228

Alfa AF: 0.236 Hom.: 2307

Bravo AF: 0.226

Asia WGS AF: 0.380 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.1
DANN	Benign	0.63

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: rs9520990; hg19: chr13-109376993; COSMIC: COSV51800419;