NM_001198950.3:c.292+9291C>T

Variant names:

• chr13-108675440-C-T
• rs9284246
• NM_001198950.3:c.292+9291C>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.292+9291C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 152,134 control chromosomes in the GnomAD database, including 35,905 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 0.68 (35905 hom., cov: 33)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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.292+9291C>T		intron	N/A	NP_001185879.1
	MYO16	NM_015011.3		c.226+9291C>T		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.292+9291C>T		intron	N/A	ENSP00000401633.3
	MYO16	ENST00000356711.7	TSL:1	c.226+9291C>T		intron	N/A	ENSP00000349145.2
	MYO16	ENST00000251041.10	TSL:5	c.226+9291C>T		intron	N/A	ENSP00000251041.5

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102962 AN: 152016 Hom.: 35843 Cov.: 33

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.678 AC: 103087 AN: 152134 Hom.: 35905 Cov.: 33 AF XY: 0.681 AC XY: 50656 AN XY: 74370

African (AFR) AF: 0.830 AC: 34489 AN: 41536

American (AMR) AF: 0.742 AC: 11335 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1938 AN: 3464

East Asian (EAS) AF: 0.738 AC: 3821 AN: 5178

South Asian (SAS) AF: 0.762 AC: 3675 AN: 4820

European-Finnish (FIN) AF: 0.571 AC: 6035 AN: 10574

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39657 AN: 67972

Other (OTH) AF: 0.664 AC: 1402 AN: 2112

Alfa AF: 0.614 Hom.: 124565

Bravo AF: 0.697

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	13
DANN	Benign	0.21
PhyloP100		1.3
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: rs9284246; hg19: chr13-109327788;