rs277828

Variant names:

• chr13-109041537-C-A
• rs277828
• NM_001198950.3:c.2797-5379C>A

Variant summary

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

The NM_001198950.3(MYO16):​c.2797-5379C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,036 control chromosomes in the GnomAD database, including 5,559 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 0.26 (5559 hom., cov: 33)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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.2797-5379C>A		intron	N/A	NP_001185879.1	F8W883
	MYO16	NM_015011.3		c.2731-5379C>A		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.2797-5379C>A		intron	N/A	ENSP00000401633.3	F8W883
	MYO16	ENST00000356711.7	TSL:1	c.2731-5379C>A		intron	N/A	ENSP00000349145.2	Q9Y6X6-1
	MYO16	ENST00000251041.10	TSL:5	c.2731-5379C>A		intron	N/A	ENSP00000251041.5	Q9Y6X6-3

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39033 AN: 151918 Hom.: 5549 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.257 AC: 39087 AN: 152036 Hom.: 5559 Cov.: 33 AF XY: 0.247 AC XY: 18324 AN XY: 74298

African (AFR) AF: 0.363 AC: 15065 AN: 41448

American (AMR) AF: 0.190 AC: 2900 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3468

East Asian (EAS) AF: 0.0203 AC: 105 AN: 5178

South Asian (SAS) AF: 0.129 AC: 622 AN: 4826

European-Finnish (FIN) AF: 0.164 AC: 1734 AN: 10554

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17144 AN: 67958

Other (OTH) AF: 0.258 AC: 544 AN: 2110

Alfa AF: 0.252 Hom.: 14917

Bravo AF: 0.266

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.065
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: rs277828; hg19: chr13-109693885;