NM_001198950.3:c.3336-2251T>G

Variant names:

• chr13-109098534-T-G
• rs156997
• NM_001198950.3:c.3336-2251T>G

Variant summary

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

The NM_001198950.3(MYO16):​c.3336-2251T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,094 control chromosomes in the GnomAD database, including 46,893 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 0.78 (46893 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 2 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=-1.08).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.83 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO16	NM_001198950.3	MANE Select	c.3336-2251T>G		intron	N/A	NP_001185879.1
	MYO16	NM_015011.3		c.3270-2251T>G		intron	N/A	NP_055826.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO16	ENST00000457511.7	TSL:1 MANE Select	c.3336-2251T>G		intron	N/A	ENSP00000401633.3
	MYO16	ENST00000356711.7	TSL:1	c.3270-2251T>G		intron	N/A	ENSP00000349145.2

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119136 AN: 151976 Hom.: 46854 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.784 AC: 119230 AN: 152094 Hom.: 46893 Cov.: 32 AF XY: 0.779 AC XY: 57939 AN XY: 74336

African (AFR) AF: 0.781 AC: 32378 AN: 41476

American (AMR) AF: 0.842 AC: 12884 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2985 AN: 3472

East Asian (EAS) AF: 0.575 AC: 2960 AN: 5150

South Asian (SAS) AF: 0.787 AC: 3784 AN: 4810

European-Finnish (FIN) AF: 0.715 AC: 7555 AN: 10570

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54057 AN: 68008

Other (OTH) AF: 0.782 AC: 1649 AN: 2108

Alfa AF: 0.793 Hom.: 6172

Bravo AF: 0.789

Asia WGS AF: 0.679 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.94
DANN	Benign	0.12
PhyloP100		-1.5
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: rs156997; hg19: chr13-109750882;