Genetic Variant MYO16:c.507+18803T>C (chr13-108746386-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001198950.3(MYO16):c.507+18803T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,064 control chromosomes in the GnomAD database, including 1,700 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 ( 1700 hom., cov: 32)

Consequence

MYO16
NM_001198950.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.435

Publications

2 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:

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new If you want to explore the variant's impact on the transcript NM_001198950.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO16	NM_001198950.3	MANE Select	c.507+18803T>C		intron	N/A	NP_001185879.1	F8W883
	MYO16	NM_015011.3		c.441+18803T>C		intron	N/A	NP_055826.1	Q9Y6X6-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYO16	ENST00000457511.7	TSL:1 MANE Select	c.507+18803T>C	intron	N/A	ENSP00000401633.3	F8W883
MYO16	ENST00000356711.7	TSL:1	c.441+18803T>C	intron	N/A	ENSP00000349145.2	Q9Y6X6-1
MYO16	ENST00000251041.10	TSL:5	c.441+18803T>C	intron	N/A	ENSP00000251041.5	Q9Y6X6-3

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21440

AN:

151948

Hom.:

1700

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0743

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.0485

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.167

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

GnomAD4 genome

AF:

0.141

AC:

21442

AN:

152064

Hom.:

1700

Cov.:

AF XY:

0.141

AC XY:

10445

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.0742

AC:

3080

AN:

41514

American (AMR)

AF:

0.160

AC:

2439

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

691

AN:

3472

East Asian (EAS)

AF:

0.0486

AC:

252

AN:

5180

South Asian (SAS)

AF:

0.134

AC:

646

AN:

4820

European-Finnish (FIN)

AF:

0.182

AC:

1914

AN:

10528

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11639

AN:

67974

Other (OTH)

AF:

0.166

AC:

349

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

921

1842

2763

3684

4605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.114

Hom.:

572

Bravo

AF:

0.142

Asia WGS

AF:

0.0870

AC:

306

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

(source)

DANN

Benign

0.72

PhyloP100

-0.43

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over