13-108804869-G-C

Variant names:

• chr13-108804869-G-C
• rs9514918
• NM_001198950.3:c.742-1810G>C

Variant summary

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

The NM_001198950.3(MYO16):​c.742-1810G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,126 control chromosomes in the GnomAD database, including 41,054 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 0.72 (41054 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO16	NM_001198950.3	c.742-1810G>C		intron_variant	Intron 6 of 34	ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000457511.7	c.742-1810G>C		intron_variant	Intron 6 of 34	1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.676-1810G>C		intron_variant	Intron 6 of 34	1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.676-1810G>C		intron_variant	Intron 6 of 24	5		ENSP00000251041.5
MYO16	ENST00000375857.6	n.62-1810G>C		intron_variant	Intron 1 of 21	2

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109914 AN: 152008 Hom.: 41020 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.723 AC: 110000 AN: 152126 Hom.: 41054 Cov.: 32 AF XY: 0.731 AC XY: 54368 AN XY: 74372

African (AFR) AF: 0.531 AC: 22025 AN: 41450

American (AMR) AF: 0.803 AC: 12272 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2935 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5170

South Asian (SAS) AF: 0.881 AC: 4245 AN: 4818

European-Finnish (FIN) AF: 0.833 AC: 8836 AN: 10604

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51892 AN: 68002

Other (OTH) AF: 0.748 AC: 1582 AN: 2114

Alfa AF: 0.691 Hom.: 2213

Bravo AF: 0.712

Asia WGS AF: 0.912 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.36
PhyloP100		-0.047
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: rs9514918; hg19: chr13-109457217;