dbSNP rs2038707: MYO16:c.5324-41G>A (chr13-109179501-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.286

Publications

7 publications found

Variant links:

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 links:

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

MYO16-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO16	NM_001198950.3 link	c.5324-41G>A		intron_variant	Intron 33 of 34	ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
MYO16	ENST00000457511.7 link	c.5324-41G>A	intron_variant	Intron 33 of 34	1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7 link	c.5258-41G>A	intron_variant	Intron 33 of 34	1		ENSP00000349145.2
MYO16-AS1	ENST00000439299.1 link	n.30-12197C>T	intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.0299

AC:

4549

AN:

152088

Hom.:

302

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.0188

AC XY:

10953

AN XY:

583092

show subpopulations

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:

AN:

53068

Middle Eastern (MID)

AF:

0.00914

AC:

AN:

5144

European-Non Finnish (NFE)

AF:

0.000386

AC:

316

AN:

819442

Other (OTH)

AF:

0.0242

AC:

1207

AN:

49934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

828

1656

2483

3311

4139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

254

508

762

1016

1270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0299

AC:

4545

AN:

152206

Hom.:

300

Cov.:

AF XY:

0.0324

AC XY:

2408

AN XY:

74406

show subpopulations

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:

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:

AN:

10578

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000515

AC:

AN:

68006

Other (OTH)

AF:

0.0246

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

198

397

595

794

992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.59

PhyloP100

0.29

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over