rs7324758

chr13-109176470-T-C

Variant summary

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

The NM_001198950.3(MYO16):c.5324-3072T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 150,384 control chromosomes in the GnomAD database, including 2,516 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 0.16 (2516 hom., cov: 27)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO16	NM_001198950.3	c.5324-3072T>C		intron_variant		ENST00000457511.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO16	ENST00000457511.7	c.5324-3072T>C		intron_variant		1	NM_001198950.3	A2
MYO16	ENST00000356711.7	c.5258-3072T>C		intron_variant		1		P2
MYO16-AS1	ENST00000439299.1	n.30-9166A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23612 AN: 150270 Hom.: 2507 Cov.: 27

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.157 AC: 23650 AN: 150384 Hom.: 2516 Cov.: 27 AF XY: 0.166 AC XY: 12153 AN XY: 73384

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.0901

Gnomad4 OTH AF: 0.148

Alfa AF: 0.128 Hom.: 139

Bravo AF: 0.171

Asia WGS AF: 0.305 AC: 1057 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.8
Dann	Benign	0.35

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: rs7324758; hg19: chr13-109828818;