NM_001198950.3:c.1249-4942C>T

Variant names:

• chr13-108850501-C-T
• rs17485138
• NM_001198950.3:c.1249-4942C>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.1249-4942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,136 control chromosomes in the GnomAD database, including 3,687 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 0.20 (3687 hom., cov: 33)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.261 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.1249-4942C>T		intron	N/A	NP_001185879.1
	MYO16	NM_015011.3		c.1183-4942C>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.1249-4942C>T		intron	N/A	ENSP00000401633.3
	MYO16	ENST00000356711.7	TSL:1	c.1183-4942C>T		intron	N/A	ENSP00000349145.2
	MYO16	ENST00000251041.10	TSL:5	c.1183-4942C>T		intron	N/A	ENSP00000251041.5

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29781 AN: 152018 Hom.: 3689 Cov.: 33

Gnomad AFR AF: 0.0520

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.196 AC: 29783 AN: 152136 Hom.: 3687 Cov.: 33 AF XY: 0.196 AC XY: 14611 AN XY: 74364

African (AFR) AF: 0.0519 AC: 2154 AN: 41524

American (AMR) AF: 0.227 AC: 3478 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3468

East Asian (EAS) AF: 0.120 AC: 623 AN: 5174

South Asian (SAS) AF: 0.142 AC: 683 AN: 4822

European-Finnish (FIN) AF: 0.256 AC: 2697 AN: 10548

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17957 AN: 67992

Other (OTH) AF: 0.241 AC: 508 AN: 2112

Alfa AF: 0.236 Hom.: 8742

Bravo AF: 0.190

Asia WGS AF: 0.124 AC: 432 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	0.43
DANN	Benign	0.28
PhyloP100		-0.93
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: rs17485138; hg19: chr13-109502849;