13-108852792-A-G

Position:

• chr13-108852792-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.1249-2651A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,972 control chromosomes in the GnomAD database, including 23,174 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 0.54 (23174 hom., cov: 31)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO16	NM_001198950.3	c.1249-2651A>G		intron_variant		ENST00000457511.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO16	ENST00000457511.7	c.1249-2651A>G		intron_variant		1	NM_001198950.3	A2
MYO16	ENST00000356711.7	c.1183-2651A>G		intron_variant		1		P2
MYO16	ENST00000251041.10	c.1183-2651A>G		intron_variant		5
MYO16	ENST00000375857.6	n.569-2651A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81745 AN: 151854 Hom.: 23159 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.538 AC: 81812 AN: 151972 Hom.: 23174 Cov.: 31 AF XY: 0.530 AC XY: 39342 AN XY: 74278

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.526

Alfa AF: 0.485 Hom.: 10243

Bravo AF: 0.555

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.016
DANN	Benign	0.42

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

Publications

LitVar

Other links and lift over

dbSNP: rs443079; hg19: chr13-109505140;