Genetic Variant MYO1B:c.3159+150G>A (chr2-191414819-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_001130158.3(MYO1B):c.3159+150G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 703,468 control chromosomes in the GnomAD database, including 736 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 ( 384 hom., cov: 33)

Exomes 𝑓: 0.026 ( 352 hom. )

Consequence

MYO1B
NM_001130158.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

1 publications found

Variant links:

Genes affected

MYO1B (HGNC:7596): (myosin IB) Enables ATP binding activity; actin filament binding activity; and microfilament motor activity. Involved in actin filament organization and post-Golgi vesicle-mediated transport. Located in several cellular components, including actin filament; endosome; and perinuclear region of cytoplasm. Colocalizes with trans-Golgi network membrane. [provided by Alliance of Genome Resources, Apr 2022]

MYO1B links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130158.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MYO1B	NM_001130158.3	MANE Select	c.3159+150G>A	intron	N/A	NP_001123630.1
MYO1B	NM_001161819.3		c.3159+150G>A	intron	N/A	NP_001155291.1
MYO1B	NM_001330237.2		c.3072+150G>A	intron	N/A	NP_001317166.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MYO1B	ENST00000392318.8	TSL:1 MANE Select	c.3159+150G>A	intron	N/A	ENSP00000376132.3
MYO1B	ENST00000304164.8	TSL:1	c.3159+150G>A	intron	N/A	ENSP00000306382.4
MYO1B	ENST00000339514.8	TSL:1	c.2985+150G>A	intron	N/A	ENSP00000341903.4

Frequencies

GnomAD3 genomes

AF:

0.0543

AC:

8262

AN:

152088

Hom.:

381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0449

Gnomad ASJ

AF:

0.0965

Gnomad EAS

AF:

0.00346

Gnomad SAS

AF:

0.0428

Gnomad FIN

AF:

0.0178

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0224

Gnomad OTH

AF:

0.0642

GnomAD4 exome

AF:

0.0259

AC:

14258

AN:

551262

Hom.:

352

AF XY:

0.0265

AC XY:

7351

AN XY:

277588

show subpopulations

African (AFR)

AF:

0.120

AC:

1565

AN:

13042

American (AMR)

AF:

0.0397

AC:

394

AN:

9916

Ashkenazi Jewish (ASJ)

AF:

0.0985

AC:

1271

AN:

12902

East Asian (EAS)

AF:

0.000696

AC:

AN:

25856

South Asian (SAS)

AF:

0.0383

AC:

947

AN:

24720

European-Finnish (FIN)

AF:

0.0179

AC:

540

AN:

30188

Middle Eastern (MID)

AF:

0.0791

AC:

202

AN:

2554

European-Non Finnish (NFE)

AF:

0.0203

AC:

8202

AN:

403800

Other (OTH)

AF:

0.0396

AC:

1119

AN:

28284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

666

1332

1998

2664

3330

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

236

472

708

944

1180

<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:

0.0544

AC:

8274

AN:

152206

Hom.:

384

Cov.:

AF XY:

0.0545

AC XY:

4052

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.124

AC:

5161

AN:

41522

American (AMR)

AF:

0.0449

AC:

686

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0965

AC:

335

AN:

3470

East Asian (EAS)

AF:

0.00347

AC:

AN:

5190

South Asian (SAS)

AF:

0.0422

AC:

203

AN:

4812

European-Finnish (FIN)

AF:

0.0178

AC:

189

AN:

10598

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0224

AC:

1523

AN:

68010

Other (OTH)

AF:

0.0636

AC:

134

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

380

760

1141

1521

1901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0404

Hom.:

Bravo

AF:

0.0597

Asia WGS

AF:

0.0340

AC:

119

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.15

(source)

DANN

Benign

0.46

PhyloP100

-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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over