rs2038707

chr13-109179501-G-Achr13-109179501-G-Cchr13-109179501-G-T

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>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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

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

GnomAD3 exomes AF: 0.0383 AC: 9549 AN: 249318 Hom.: 880 AF XY: 0.0373 AC XY: 5020 AN XY: 134620

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 SAS exome AF: 0.0617

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

Gnomad4 AFR exome AF: 0.0504

Gnomad4 AMR exome AF: 0.0343

Gnomad4 ASJ exome AF: 0.00668

Gnomad4 EAS exome AF: 0.284

Gnomad4 SAS exome AF: 0.0601

Gnomad4 FIN exome AF: 0.000358

Gnomad4 NFE exome AF: 0.000386

Gnomad4 OTH exome AF: 0.0242

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

Gnomad4 AFR AF: 0.0504

Gnomad4 AMR AF: 0.0356

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.0692

Gnomad4 FIN AF: 0.000756

Gnomad4 NFE AF: 0.000515

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.00405 Hom.: 208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.4
Dann	Benign	0.59

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;