chr20-34991096-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_020884.7(MYH7B):c.2158T>C(p.Leu720Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 1,611,862 control chromosomes in the GnomAD database, including 429,391 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.77 ( 45513 hom., cov: 33)

Exomes 𝑓: 0.72 ( 383878 hom. )

Consequence

MYH7B
NM_020884.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.09

Publications

20 publications found

Variant links:

Genes affected

MYH7B (HGNC:15906): (myosin heavy chain 7B) The myosin II molecule is a multi-subunit complex consisting of two heavy chains and four light chains. This gene encodes a heavy chain of myosin II, which is a member of the motor-domain superfamily. The heavy chain includes a globular motor domain, which catalyzes ATP hydrolysis and interacts with actin, and a tail domain in which heptad repeat sequences promote dimerization by interacting to form a rod-like alpha-helical coiled coil. This heavy chain subunit is a slow-twitch myosin. Alternatively spliced transcript variants have been found, but the full-length nature of these variants is not determined. [provided by RefSeq, Mar 2010]

MYH7B Gene-Disease associations (from GenCC):

left ventricular noncompaction
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

MYH7B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 20-34991096-T-C is Benign according to our data. Variant chr20-34991096-T-C is described in CliVar as Benign. Clinvar id is 1601513.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-34991096-T-C is described in CliVar as Benign. Clinvar id is 1601513.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-34991096-T-C is described in CliVar as Benign. Clinvar id is 1601513.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-34991096-T-C is described in CliVar as Benign. Clinvar id is 1601513.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-34991096-T-C is described in CliVar as Benign. Clinvar id is 1601513.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH7B	NM_020884.7 link	c.2158T>C	p.Leu720Leu	synonymous_variant	Exon 24 of 45	ENST00000262873.13	NP_065935.4	A7E2Y1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH7B	ENST00000262873.13 link	c.2158T>C	p.Leu720Leu	synonymous_variant	Exon 24 of 45	1	NM_020884.7	ENSP00000262873.8		A0A6E1W127

Frequencies

GnomAD3 genomes

AF:

0.770

AC:

117147

AN:

152060

Hom.:

45465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.823

Gnomad AMI

AF:

0.872

Gnomad AMR

AF:

0.821

Gnomad ASJ

AF:

0.798

Gnomad EAS

AF:

0.776

Gnomad SAS

AF:

0.705

Gnomad FIN

AF:

0.802

Gnomad MID

AF:

0.829

Gnomad NFE

AF:

0.723

Gnomad OTH

AF:

0.783

GnomAD2 exomes

AF:

0.768

AC:

189964

AN:

247492

AF XY:

0.761

show subpopulations

Gnomad AFR exome

AF:

0.825

Gnomad AMR exome

AF:

0.891

Gnomad ASJ exome

AF:

0.792

Gnomad EAS exome

AF:

0.761

Gnomad FIN exome

AF:

0.792

Gnomad NFE exome

AF:

0.730

Gnomad OTH exome

AF:

0.783

GnomAD4 exome

AF:

0.723

AC:

1055837

AN:

1459684

Hom.:

383878

Cov.:

AF XY:

0.724

AC XY:

525448

AN XY:

726072

show subpopulations

African (AFR)

AF:

0.825

AC:

27615

AN:

33454

American (AMR)

AF:

0.885

AC:

39446

AN:

44574

Ashkenazi Jewish (ASJ)

AF:

0.794

AC:

20627

AN:

25972

East Asian (EAS)

AF:

0.789

AC:

31332

AN:

39686

South Asian (SAS)

AF:

0.713

AC:

61290

AN:

86002

European-Finnish (FIN)

AF:

0.792

AC:

42237

AN:

53304

Middle Eastern (MID)

AF:

0.869

AC:

4997

AN:

5750

European-Non Finnish (NFE)

AF:

0.706

AC:

783995

AN:

1110642

Other (OTH)

AF:

0.735

AC:

44298

AN:

60300

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

13573

27146

40720

54293

67866

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19730

39460

59190

78920

98650

<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:

0.771

AC:

117255

AN:

152178

Hom.:

45513

Cov.:

AF XY:

0.774

AC XY:

57591

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.823

AC:

34156

AN:

41520

American (AMR)

AF:

0.822

AC:

12562

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.798

AC:

2769

AN:

3470

East Asian (EAS)

AF:

0.775

AC:

4004

AN:

5166

South Asian (SAS)

AF:

0.706

AC:

3405

AN:

4826

European-Finnish (FIN)

AF:

0.802

AC:

8508

AN:

10608

Middle Eastern (MID)

AF:

0.830

AC:

244

AN:

294

European-Non Finnish (NFE)

AF:

0.723

AC:

49153

AN:

67978

Other (OTH)

AF:

0.785

AC:

1659

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1428

2855

4283

5710

7138

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

852

1704

2556

3408

4260

<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:

0.752

Hom.:

21004

Bravo

AF:

0.780

Asia WGS

AF:

0.766

AC:

2664

AN:

3478

EpiCase

AF:

0.739

EpiControl

AF:

0.745

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

9.8

(source)

DANN

Benign

0.79

PhyloP100

2.1

Mutation Taster

=98/2

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over