Variant 20-34991096-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_020884.7(MYH7B):c.2158T>C(p.Leu720=) 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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 ClinVar 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/exons	MANE	Protein	UniProt
MYH7B	NM_020884.7 linkuse as main transcript	c.2158T>C	p.Leu720=	synonymous_variant	24/45	ENST00000262873.13	NP_065935.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYH7B	ENST00000262873.13 linkuse as main transcript	c.2158T>C	p.Leu720=	synonymous_variant	24/45	1	NM_020884.7	ENSP00000262873	P1

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

GnomAD3 exomes

AF:

0.768

AC:

189964

AN:

247492

Hom.:

73504

AF XY:

0.761

AC XY:

102259

AN XY:

134288

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 SAS exome

AF:

0.712

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

Gnomad4 AFR exome

AF:

0.825

Gnomad4 AMR exome

AF:

0.885

Gnomad4 ASJ exome

AF:

0.794

Gnomad4 EAS exome

AF:

0.789

Gnomad4 SAS exome

AF:

0.713

Gnomad4 FIN exome

AF:

0.792

Gnomad4 NFE exome

AF:

0.706

Gnomad4 OTH exome

AF:

0.735

GnomAD4 genome

AF:

0.771

AC:

117255

AN:

152178

Hom.:

45513

Cov.:

AF XY:

0.774

AC XY:

57591

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.823

Gnomad4 AMR

AF:

0.822

Gnomad4 ASJ

AF:

0.798

Gnomad4 EAS

AF:

0.775

Gnomad4 SAS

AF:

0.706

Gnomad4 FIN

AF:

0.802

Gnomad4 NFE

AF:

0.723

Gnomad4 OTH

AF:

0.785

Alfa

AF:

0.745

Hom.:

19133

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

9.8

DANN

Benign

0.79

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over