ENST00000356711.7:c.-39+13792C>T

Variant names:

• chr13-108610031-C-T
• rs4238264
• ENST00000356711.7:c.-39+13792C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000356711.7(MYO16):​c.-39+13792C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 151,982 control chromosomes in the GnomAD database, including 38,348 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 0.71 (38348 hom., cov: 30)
• Consequence: MYO16 ENST00000356711.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000356711.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO16	NM_015011.3		c.-39+13792C>T		intron	N/A	NP_055826.1	Q9Y6X6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO16	ENST00000356711.7	TSL:1	c.-39+13792C>T		intron	N/A	ENSP00000349145.2	Q9Y6X6-1
	MYO16	ENST00000251041.10	TSL:5	c.-39+13792C>T		intron	N/A	ENSP00000251041.5	Q9Y6X6-3

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107638 AN: 151864 Hom.: 38322 Cov.: 30

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.709 AC: 107714 AN: 151982 Hom.: 38348 Cov.: 30 AF XY: 0.708 AC XY: 52595 AN XY: 74278

African (AFR) AF: 0.676 AC: 28013 AN: 41450

American (AMR) AF: 0.724 AC: 11056 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2687 AN: 3464

East Asian (EAS) AF: 0.552 AC: 2845 AN: 5154

South Asian (SAS) AF: 0.701 AC: 3370 AN: 4804

European-Finnish (FIN) AF: 0.701 AC: 7402 AN: 10552

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49812 AN: 67980

Other (OTH) AF: 0.719 AC: 1514 AN: 2106

Alfa AF: 0.731 Hom.: 23941

Bravo AF: 0.708

Asia WGS AF: 0.644 AC: 2243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.023
DANN	Benign	0.57
PhyloP100		-3.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4238264; hg19: chr13-109262379;