13-108820501-A-G

Position:

• chr13-108820501-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001198950.3(MYO16):​c.943+89A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 1,074,734 control chromosomes in the GnomAD database, including 504,930 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 0.85 (58721 hom., cov: 31)
  • Exomes 𝑓: 0.98 (446209 hom.)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

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]

MYO16 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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/exons	MANE	Protein	UniProt
MYO16	NM_001198950.3	c.943+89A>G		intron_variant		ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000457511.7	c.943+89A>G		intron_variant		1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.877+89A>G		intron_variant		1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.877+89A>G		intron_variant		5		ENSP00000251041.5
MYO16	ENST00000375857.6	n.263+89A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129075 AN: 151998 Hom.: 58707 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.885

GnomAD4 exome AF: 0.980 AC: 904196 AN: 922618 Hom.: 446209 AF XY: 0.982 AC XY: 464667 AN XY: 473188

Gnomad4 AFR exome AF: 0.476

Gnomad4 AMR exome AF: 0.966

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.987

Gnomad4 SAS exome AF: 0.975

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.998

Gnomad4 OTH exome AF: 0.956

GnomAD4 genome AF: 0.849 AC: 129129 AN: 152116 Hom.: 58721 Cov.: 31 AF XY: 0.853 AC XY: 63470 AN XY: 74392

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.976

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.997

Gnomad4 OTH AF: 0.886

Alfa AF: 0.944 Hom.: 21594

Bravo AF: 0.828

Asia WGS AF: 0.940 AC: 3269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.058
DANN	Benign	0.41
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9521065; hg19: chr13-109472849;