rs9514923

Variant names:

• chr13-108814281-A-G
• rs9514923
• NM_001198950.3:c.868-6056A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-108814281-A-G
• chr13-108814281-A-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.868-6056A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,152 control chromosomes in the GnomAD database, including 59,495 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 0.86 (59495 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO16	NM_001198950.3	c.868-6056A>G		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.868-6056A>G		intron_variant	Intron 7 of 34	1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.802-6056A>G		intron_variant	Intron 7 of 34	1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.802-6056A>G		intron_variant	Intron 7 of 24	5		ENSP00000251041.5
MYO16	ENST00000375857.6	n.188-6056A>G		intron_variant	Intron 2 of 21	2

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130588 AN: 152034 Hom.: 59486 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.859 AC: 130631 AN: 152152 Hom.: 59495 Cov.: 32 AF XY: 0.862 AC XY: 64156 AN XY: 74406

African (AFR) AF: 0.520 AC: 21562 AN: 41452

American (AMR) AF: 0.936 AC: 14293 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3467 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5114 AN: 5180

South Asian (SAS) AF: 0.976 AC: 4712 AN: 4828

European-Finnish (FIN) AF: 0.999 AC: 10604 AN: 10612

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67798 AN: 68014

Other (OTH) AF: 0.893 AC: 1889 AN: 2116

Alfa AF: 0.901 Hom.: 7909

Bravo AF: 0.839

Asia WGS AF: 0.941 AC: 3265 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.013
DANN	Benign	0.45
PhyloP100		-2.8
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: rs9514923; hg19: chr13-109466629;