13-109172580-C-T

Variant names:

• chr13-109172580-C-T
• rs4976845
• NM_001198950.3:c.5324-6962C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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]

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

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 = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001198950.3. 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_001198950.3	MANE Select	c.5324-6962C>T		intron	N/A	NP_001185879.1	F8W883
	MYO16	NM_015011.3		c.5258-6962C>T		intron	N/A	NP_055826.1	Q9Y6X6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO16	ENST00000457511.7	TSL:1 MANE Select	c.5324-6962C>T		intron	N/A	ENSP00000401633.3	F8W883
	MYO16	ENST00000356711.7	TSL:1	c.5258-6962C>T		intron	N/A	ENSP00000349145.2	Q9Y6X6-1
	MYO16-AS1	ENST00000439299.1	TSL:5	n.30-5276G>A		intron	N/A

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

African (AFR) AF: 0.126 AC: 5237 AN: 41468

American (AMR) AF: 0.386 AC: 5885 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3472

East Asian (EAS) AF: 0.134 AC: 691 AN: 5166

South Asian (SAS) AF: 0.345 AC: 1663 AN: 4824

European-Finnish (FIN) AF: 0.402 AC: 4244 AN: 10552

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33433 AN: 67942

Other (OTH) AF: 0.372 AC: 788 AN: 2116

Alfa AF: 0.435 Hom.: 48294

Bravo AF: 0.342

Asia WGS AF: 0.262 AC: 911 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	1.2
DANN	Benign	0.51
PhyloP100		-0.83
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: rs4976845; hg19: chr13-109824928;