rs726449

Variant names:

• chr13-108499141-C-T
• rs726449
• XM_011521062.2:c.-39+3217C>T

Variant summary

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

The ENST00000757457.1(ENSG00000298702):​n.43+3217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,148 control chromosomes in the GnomAD database, including 6,320 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 0.28 (6320 hom., cov: 33)
• Consequence: ENSG00000298702 ENST00000757457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• 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]

ENSG00000298702 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757457.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298702	ENST00000757457.1		n.43+3217C>T		intron	N/A
	ENSG00000298702	ENST00000757458.1		n.91+3142C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42087 AN: 152030 Hom.: 6322 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.277 AC: 42085 AN: 152148 Hom.: 6320 Cov.: 33 AF XY: 0.271 AC XY: 20135 AN XY: 74368

African (AFR) AF: 0.180 AC: 7487 AN: 41522

American (AMR) AF: 0.263 AC: 4015 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3470

East Asian (EAS) AF: 0.177 AC: 917 AN: 5178

South Asian (SAS) AF: 0.143 AC: 692 AN: 4824

European-Finnish (FIN) AF: 0.296 AC: 3127 AN: 10566

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23932 AN: 67988

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.316 Hom.: 4425

Bravo AF: 0.275

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.60
PhyloP100		0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs726449;

hg19: chr13-109151489;