NM_001198950.3:c.867+1154G>A

Variant names:

• chr13-108807958-G-A
• rs8002448
• NM_001198950.3:c.867+1154G>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.867+1154G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,094 control chromosomes in the GnomAD database, including 41,218 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 (41218 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• 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=-0.99).
• 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.867+1154G>A		intron_variant	Intron 7 of 34	ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000457511.7	c.867+1154G>A		intron_variant	Intron 7 of 34	1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.801+1154G>A		intron_variant	Intron 7 of 34	1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.801+1154G>A		intron_variant	Intron 7 of 24	5		ENSP00000251041.5
MYO16	ENST00000375857.6	n.187+1154G>A		intron_variant	Intron 2 of 21	2

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110128 AN: 151978 Hom.: 41186 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.725 AC: 110212 AN: 152094 Hom.: 41218 Cov.: 32 AF XY: 0.733 AC XY: 54485 AN XY: 74356

African (AFR) AF: 0.532 AC: 22028 AN: 41432

American (AMR) AF: 0.806 AC: 12312 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2933 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5183 AN: 5186

South Asian (SAS) AF: 0.880 AC: 4249 AN: 4830

European-Finnish (FIN) AF: 0.834 AC: 8836 AN: 10596

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52041 AN: 67994

Other (OTH) AF: 0.750 AC: 1584 AN: 2112

Alfa AF: 0.757 Hom.: 56525

Bravo AF: 0.714

Asia WGS AF: 0.911 AC: 3167 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
DANN	Benign	0.22
PhyloP100		-2.0
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: rs8002448; hg19: chr13-109460306;