13-108858711-T-G

Position:

• chr13-108858711-T-G

Variant summary

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

The ENST00000457511.7(MYO16):​c.1359+3158T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,184 control chromosomes in the GnomAD database, including 1,697 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 0.14 (1697 hom., cov: 32)
• Consequence: MYO16 ENST00000457511.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO16	NM_001198950.3	c.1359+3158T>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.1359+3158T>G		intron_variant		1	NM_001198950.3	ENSP00000401633	A2

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21555 AN: 152066 Hom.: 1689 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.142 AC: 21590 AN: 152184 Hom.: 1697 Cov.: 32 AF XY: 0.144 AC XY: 10700 AN XY: 74398

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.0834

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.134

Alfa AF: 0.135 Hom.: 683

Bravo AF: 0.142

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.48

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: rs814141; hg19: chr13-109511059;