dbSNP rs257048: MYO10:c.3800+113C>T (chr5-16694258-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_012334.3(MYO10):c.3800+113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 1,501,132 control chromosomes in the GnomAD database, including 1,190 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 0.054 ( 637 hom., cov: 33)

Exomes 𝑓: 0.0091 ( 553 hom. )

Consequence

MYO10
NM_012334.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.977

Publications

1 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO10	NM_012334.3 link	c.3800+113C>T		intron_variant	Intron 27 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.3800+113C>T	intron_variant	Intron 27 of 40	1	NM_012334.3	ENSP00000421280.1	Q9HD67-1
MYO10	ENST00000274203.13 link	c.3833+113C>T	intron_variant	Intron 27 of 40	5		ENSP00000274203.10	A0A0A0MQX1
MYO10	ENST00000505695.5 link	c.1817+113C>T	intron_variant	Intron 9 of 22	2		ENSP00000421170.1	E9PEW5
MYO10	ENST00000515803.5 link	c.1817+113C>T	intron_variant	Intron 9 of 22	2		ENSP00000425051.1	E9PEW5

Frequencies

GnomAD3 genomes

AF:

0.0537

AC:

8176

AN:

152180

Hom.:

635

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0234

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.00607

Gnomad OTH

AF:

0.0406

GnomAD4 exome

AF:

0.00906

AC:

12219

AN:

1348834

Hom.:

553

AF XY:

0.00838

AC XY:

5591

AN XY:

667480

show subpopulations

African (AFR)

AF:

0.179

AC:

5463

AN:

30508

American (AMR)

AF:

0.0152

AC:

574

AN:

37754

Ashkenazi Jewish (ASJ)

AF:

0.0142

AC:

308

AN:

21650

East Asian (EAS)

AF:

0.000154

AC:

AN:

38886

South Asian (SAS)

AF:

0.00134

AC:

100

AN:

74540

European-Finnish (FIN)

AF:

0.000875

AC:

AN:

47988

Middle Eastern (MID)

AF:

0.0314

AC:

134

AN:

4274

European-Non Finnish (NFE)

AF:

0.00447

AC:

4635

AN:

1037332

Other (OTH)

AF:

0.0171

AC:

957

AN:

55902

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

560

1120

1681

2241

2801

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

258

516

774

1032

1290

<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:

0.0539

AC:

8203

AN:

152298

Hom.:

637

Cov.:

AF XY:

0.0518

AC XY:

3856

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.175

AC:

7254

AN:

41544

American (AMR)

AF:

0.0234

AC:

358

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0107

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5182

South Asian (SAS)

AF:

0.00104

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.000282

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00607

AC:

413

AN:

68036

Other (OTH)

AF:

0.0411

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

357

713

1070

1426

1783

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0167

Hom.:

Bravo

AF:

0.0614

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

0.98

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