chr13-109179501-G-A

Variant names:

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

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>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0192 in 1,292,666 control chromosomes in the GnomAD database, including 2,163 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 0.030 (300 hom., cov: 33)
  • Exomes 𝑓: 0.018 (1863 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 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>A		intron	N/A	NP_001185879.1
	MYO16	NM_015011.3		c.5258-41G>A		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>A		intron	N/A	ENSP00000401633.3
	MYO16	ENST00000356711.7	TSL:1	c.5258-41G>A		intron	N/A	ENSP00000349145.2
	MYO16-AS1	ENST00000439299.1	TSL:5	n.30-12197C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0299 AC: 4549 AN: 152088 Hom.: 302 Cov.: 33

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.000756

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000515

Gnomad OTH AF: 0.0249

GnomAD2 exomes AF: 0.0383 AC: 9549 AN: 249318 AF XY: 0.0373

Gnomad AFR exome AF: 0.0540

Gnomad AMR exome AF: 0.0341

Gnomad ASJ exome AF: 0.00529

Gnomad EAS exome AF: 0.292

Gnomad FIN exome AF: 0.000465

Gnomad NFE exome AF: 0.000622

Gnomad OTH exome AF: 0.0240

GnomAD4 exome AF: 0.0177 AC: 20226 AN: 1140460 Hom.: 1863 Cov.: 15 AF XY: 0.0188 AC XY: 10953 AN XY: 583092

African (AFR) AF: 0.0504 AC: 1362 AN: 27020

American (AMR) AF: 0.0343 AC: 1513 AN: 44154

Ashkenazi Jewish (ASJ) AF: 0.00668 AC: 161 AN: 24118

East Asian (EAS) AF: 0.284 AC: 10824 AN: 38116

South Asian (SAS) AF: 0.0601 AC: 4777 AN: 79464

European-Finnish (FIN) AF: 0.000358 AC: 19 AN: 53068

Middle Eastern (MID) AF: 0.00914 AC: 47 AN: 5144

European-Non Finnish (NFE) AF: 0.000386 AC: 316 AN: 819442

Other (OTH) AF: 0.0242 AC: 1207 AN: 49934

GnomAD4 genome AF: 0.0299 AC: 4545 AN: 152206 Hom.: 300 Cov.: 33 AF XY: 0.0324 AC XY: 2408 AN XY: 74406

African (AFR) AF: 0.0504 AC: 2095 AN: 41544

American (AMR) AF: 0.0356 AC: 545 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1447 AN: 5172

South Asian (SAS) AF: 0.0692 AC: 333 AN: 4810

European-Finnish (FIN) AF: 0.000756 AC: 8 AN: 10578

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.000515 AC: 35 AN: 68006

Other (OTH) AF: 0.0246 AC: 52 AN: 2112

Alfa AF: 0.00405 Hom.: 208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.59
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;