chr13-108820501-A-G

Variant names:

• chr13-108820501-A-G
• rs9521065
• NM_001198950.3:c.943+89A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.91).
• 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 rank	MANE	Protein	UniProt
MYO16	NM_001198950.3	c.943+89A>G		intron_variant	Intron 8 of 34	ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000457511.7	c.943+89A>G		intron_variant	Intron 8 of 34	1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.877+89A>G		intron_variant	Intron 8 of 34	1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.877+89A>G		intron_variant	Intron 8 of 24	5		ENSP00000251041.5
MYO16	ENST00000375857.6	n.263+89A>G		intron_variant	Intron 3 of 21	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

African (AFR) AF: 0.476 AC: 10637 AN: 22340

American (AMR) AF: 0.966 AC: 33613 AN: 34796

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 21611 AN: 21618

East Asian (EAS) AF: 0.987 AC: 32950 AN: 33374

South Asian (SAS) AF: 0.975 AC: 66977 AN: 68688

European-Finnish (FIN) AF: 1.00 AC: 47098 AN: 47116

Middle Eastern (MID) AF: 0.968 AC: 4594 AN: 4744

European-Non Finnish (NFE) AF: 0.998 AC: 646342 AN: 647718

Other (OTH) AF: 0.956 AC: 40374 AN: 42224

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

African (AFR) AF: 0.486 AC: 20101 AN: 41402

American (AMR) AF: 0.933 AC: 14246 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3467 AN: 3470

East Asian (EAS) AF: 0.988 AC: 5108 AN: 5172

South Asian (SAS) AF: 0.976 AC: 4713 AN: 4830

European-Finnish (FIN) AF: 0.999 AC: 10614 AN: 10622

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

European-Non Finnish (NFE) AF: 0.997 AC: 67814 AN: 68028

Other (OTH) AF: 0.886 AC: 1874 AN: 2116

Alfa AF: 0.942 Hom.: 25411

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
PhyloP100		-0.20
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9521065; hg19: chr13-109472849;