rs4976845

chr13-109172580-C-T

Variant summary

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

The NM_001198950.3(MYO16):c.5324-6962C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,008 control chromosomes in the GnomAD database, including 11,705 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 0.35 (11705 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

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]

MYO16-AS1 (HGNC:39913): (MYO16 antisense RNA 1)

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 = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO16	NM_001198950.3	c.5324-6962C>T		intron_variant		ENST00000457511.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO16	ENST00000457511.7	c.5324-6962C>T		intron_variant		1	NM_001198950.3	A2
MYO16	ENST00000356711.7	c.5258-6962C>T		intron_variant		1		P2
MYO16-AS1	ENST00000439299.1	n.30-5276G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53914 AN: 151890 Hom.: 11704 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.355 AC: 53918 AN: 152008 Hom.: 11705 Cov.: 32 AF XY: 0.349 AC XY: 25935 AN XY: 74288

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.372

Alfa AF: 0.460 Hom.: 22303

Bravo AF: 0.342

Asia WGS AF: 0.262 AC: 911 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	1.2
Dann	Benign	0.51

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: rs4976845; hg19: chr13-109824928;