13-109179501-G-C

Variant names:

• chr13-109179501-G-C
• rs2038707
• NM_001198950.3:c.5324-41G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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]

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

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 (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001198950.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO16	NM_001198950.3	MANE Select	c.5324-41G>C		intron	N/A	NP_001185879.1
	MYO16	NM_015011.3		c.5258-41G>C		intron	N/A	NP_055826.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO16	ENST00000457511.7	TSL:1 MANE Select	c.5324-41G>C		intron	N/A	ENSP00000401633.3
	MYO16	ENST00000356711.7	TSL:1	c.5258-41G>C		intron	N/A	ENSP00000349145.2
	MYO16-AS1	ENST00000439299.1	TSL:5	n.30-12197C>G		intron	N/A

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

GnomAD2 exomes AF: 0.177 AC: 44166 AN: 249318 AF XY: 0.175

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 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

African (AFR) AF: 0.0566 AC: 1529 AN: 27014

American (AMR) AF: 0.176 AC: 7769 AN: 44134

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 3267 AN: 24104

East Asian (EAS) AF: 0.279 AC: 10628 AN: 38114

South Asian (SAS) AF: 0.160 AC: 12691 AN: 79444

European-Finnish (FIN) AF: 0.297 AC: 15752 AN: 53018

Middle Eastern (MID) AF: 0.129 AC: 663 AN: 5140

European-Non Finnish (NFE) AF: 0.155 AC: 127042 AN: 818430

Other (OTH) AF: 0.165 AC: 8217 AN: 49884

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

African (AFR) AF: 0.0619 AC: 2573 AN: 41538

American (AMR) AF: 0.155 AC: 2378 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1425 AN: 5172

South Asian (SAS) AF: 0.172 AC: 827 AN: 4814

European-Finnish (FIN) AF: 0.301 AC: 3181 AN: 10568

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10677 AN: 68004

Other (OTH) AF: 0.160 AC: 337 AN: 2112

Alfa AF: 0.102 Hom.: 208

Bravo AF: 0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.39
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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