rs4238264

Variant names:

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

Variant summary

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

The NM_015011.3(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 NM_015011.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO16	NM_015011.3	c.-39+13792C>T		intron_variant	Intron 1 of 34		NP_055826.1
MYO16	XM_011521062.2	c.-38-55855C>T		intron_variant	Intron 1 of 34		XP_011519364.1
MYO16	XM_047430183.1	c.-38-55855C>T		intron_variant	Intron 1 of 34		XP_047286139.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000356711.7	c.-39+13792C>T		intron_variant	Intron 1 of 34	1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.-39+13792C>T		intron_variant	Intron 1 of 24	5		ENSP00000251041.5

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

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.719

Alfa AF: 0.732 Hom.: 21715

Bravo AF: 0.708

Asia WGS AF: 0.644 AC: 2243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.023
DANN	Benign	0.57

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: rs4238264; hg19: chr13-109262379;