13-109179501-G-C

Position:

• chr13-109179501-G-C

Variant summary

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

The NM_001198950.3(MYO16):​c.5324-41G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,291,472 control chromosomes in the GnomAD database, including 18,799 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 0.14 (1992 hom., cov: 33)
  • Exomes 𝑓: 0.16 (16807 hom.)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

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-AS1 (HGNC:39913): (MYO16 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO16	NM_001198950.3	c.5324-41G>C		intron_variant		ENST00000457511.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO16	ENST00000457511.7	c.5324-41G>C		intron_variant		1	NM_001198950.3	A2
MYO16	ENST00000356711.7	c.5258-41G>C		intron_variant		1		P2
MYO16-AS1	ENST00000439299.1	n.30-12197C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21988 AN: 152072 Hom.: 1987 Cov.: 33

Gnomad AFR AF: 0.0620

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.157

GnomAD3 exomes AF: 0.177 AC: 44166 AN: 249318 Hom.: 4296 AF XY: 0.175 AC XY: 23600 AN XY: 134620

Gnomad AFR exome AF: 0.0600

Gnomad AMR exome AF: 0.175

Gnomad ASJ exome AF: 0.130

Gnomad EAS exome AF: 0.274

Gnomad SAS exome AF: 0.161

Gnomad FIN exome AF: 0.306

Gnomad NFE exome AF: 0.163

Gnomad OTH exome AF: 0.171

GnomAD4 exome AF: 0.165 AC: 187558 AN: 1139282 Hom.: 16807 Cov.: 15 AF XY: 0.165 AC XY: 95985 AN XY: 582540

Gnomad4 AFR exome AF: 0.0566

Gnomad4 AMR exome AF: 0.176

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.279

Gnomad4 SAS exome AF: 0.160

Gnomad4 FIN exome AF: 0.297

Gnomad4 NFE exome AF: 0.155

Gnomad4 OTH exome AF: 0.165

GnomAD4 genome AF: 0.145 AC: 22002 AN: 152190 Hom.: 1992 Cov.: 33 AF XY: 0.152 AC XY: 11275 AN XY: 74392

Gnomad4 AFR AF: 0.0619

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.160

Alfa AF: 0.102 Hom.: 208

Bravo AF: 0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.39

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: rs2038707; hg19: chr13-109831849; COSMIC: COSV62759370;