Genetic Variant MYO10:c.3991-65A>G (chr5-16684000-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_012334.3(MYO10):c.3991-65A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 1,432,588 control chromosomes in the GnomAD database, including 63,851 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 0.28 ( 6080 hom., cov: 32)

Exomes 𝑓: 0.30 ( 57771 hom. )

Consequence

MYO10
NM_012334.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.69

Publications

6 publications found

Variant links:

Genes affected

MYO10 (HGNC:7593): (myosin X) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional non-muscle myosin-10 (MYH10). Unconventional myosins contain the basic domains of conventional myosins and are further distinguished from class members by their tail domains. This gene functions as an actin-based molecular motor and plays a role in integration of F-actin and microtubule cytoskeletons during meiosis. [provided by RefSeq, Dec 2011]

MYO10 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO10	NM_012334.3 link	c.3991-65A>G		intron_variant	Intron 29 of 40	ENST00000513610.6	NP_036466.2	Q9HD67-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MYO10	ENST00000513610.6 link	c.3991-65A>G	intron_variant	Intron 29 of 40	1	NM_012334.3	ENSP00000421280.1	Q9HD67-1
MYO10	ENST00000274203.13 link	c.4024-65A>G	intron_variant	Intron 29 of 40	5		ENSP00000274203.10	A0A0A0MQX1
MYO10	ENST00000505695.5 link	c.2008-65A>G	intron_variant	Intron 11 of 22	2		ENSP00000421170.1	E9PEW5
MYO10	ENST00000515803.5 link	c.2008-65A>G	intron_variant	Intron 11 of 22	2		ENSP00000425051.1	E9PEW5

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42644

AN:

151972

Hom.:

6069

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.290

Gnomad EAS

AF:

0.253

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.268

GnomAD4 exome

AF:

0.298

AC:

382051

AN:

1280496

Hom.:

57771

AF XY:

0.300

AC XY:

192981

AN XY:

642760

show subpopulations

African (AFR)

AF:

0.249

AC:

7374

AN:

29562

American (AMR)

AF:

0.293

AC:

11596

AN:

39590

Ashkenazi Jewish (ASJ)

AF:

0.288

AC:

7070

AN:

24524

East Asian (EAS)

AF:

0.262

AC:

9800

AN:

37466

South Asian (SAS)

AF:

0.379

AC:

29985

AN:

79220

European-Finnish (FIN)

AF:

0.317

AC:

16301

AN:

51392

Middle Eastern (MID)

AF:

0.242

AC:

1325

AN:

5478

European-Non Finnish (NFE)

AF:

0.294

AC:

282148

AN:

958842

Other (OTH)

AF:

0.302

AC:

16452

AN:

54422

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

13178

26355

39533

52710

65888

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8988

17976

26964

35952

44940

<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:

0.281

AC:

42677

AN:

152092

Hom.:

6080

Cov.:

AF XY:

0.282

AC XY:

20956

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.260

AC:

10787

AN:

41492

American (AMR)

AF:

0.264

AC:

4041

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.290

AC:

1006

AN:

3472

East Asian (EAS)

AF:

0.252

AC:

1304

AN:

5166

South Asian (SAS)

AF:

0.365

AC:

1757

AN:

4818

European-Finnish (FIN)

AF:

0.332

AC:

3505

AN:

10570

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19323

AN:

67978

Other (OTH)

AF:

0.271

AC:

573

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1554

3109

4663

6218

7772

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

442

884

1326

1768

2210

<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:

0.280

Hom.:

1280

Bravo

AF:

0.276

Asia WGS

AF:

0.289

AC:

1005

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.0070

(source)

DANN

Benign

0.50

PhyloP100

-3.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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