Variant chr20-34977677-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020884.7(MYH7B):c.-76C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,471,412 control chromosomes in the GnomAD database, including 65,229 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 5976 hom., cov: 23)

Exomes 𝑓: 0.30 ( 59253 hom. )

Consequence

MYH7B
NM_020884.7 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0670

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 20-34977677-C-T is Benign according to our data. Variant chr20-34977677-C-T is described in ClinVar as [Benign]. Clinvar id is 1543896.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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.-76C>T		5_prime_UTR_variant	4/45	ENST00000262873.13	NP_065935.4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
MYH7B	ENST00000262873.13 linkuse as main transcript	c.-76C>T	5_prime_UTR_variant	4/45	1	NM_020884.7	ENSP00000262873	P1
MYH7B	ENST00000470929.5 linkuse as main transcript	n.11C>T	non_coding_transcript_exon_variant	1/6	2
MYH7B	ENST00000673749.1 linkuse as main transcript	n.459C>T	non_coding_transcript_exon_variant	4/9

Frequencies

GnomAD3 genomes

AF:

0.330

AC:

41147

AN:

124708

Hom.:

5976

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.227

Gnomad EAS

AF:

0.293

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.310

GnomAD3 exomes

AF:

0.238

AC:

45683

AN:

191614

Hom.:

5843

AF XY:

0.241

AC XY:

24682

AN XY:

102392

show subpopulations

Gnomad AFR exome

AF:

0.322

Gnomad AMR exome

AF:

0.121

Gnomad ASJ exome

AF:

0.202

Gnomad EAS exome

AF:

0.234

Gnomad SAS exome

AF:

0.285

Gnomad FIN exome

AF:

0.212

Gnomad NFE exome

AF:

0.263

Gnomad OTH exome

AF:

0.217

GnomAD4 exome

AF:

0.301

AC:

405124

AN:

1346640

Hom.:

59253

Cov.:

AF XY:

0.300

AC XY:

199435

AN XY:

665150

show subpopulations

Gnomad4 AFR exome

AF:

0.353

Gnomad4 AMR exome

AF:

0.140

Gnomad4 ASJ exome

AF:

0.233

Gnomad4 EAS exome

AF:

0.277

Gnomad4 SAS exome

AF:

0.289

Gnomad4 FIN exome

AF:

0.243

Gnomad4 NFE exome

AF:

0.311

Gnomad4 OTH exome

AF:

0.303

GnomAD4 genome

AF:

0.330

AC:

41161

AN:

124772

Hom.:

5976

Cov.:

AF XY:

0.331

AC XY:

19640

AN XY:

59300

show subpopulations

Gnomad4 AFR

AF:

0.396

Gnomad4 AMR

AF:

0.287

Gnomad4 ASJ

AF:

0.227

Gnomad4 EAS

AF:

0.293

Gnomad4 SAS

AF:

0.348

Gnomad4 FIN

AF:

0.305

Gnomad4 NFE

AF:

0.313

Gnomad4 OTH

AF:

0.307

Alfa

AF:

0.271

Hom.:

11593

Bravo

AF:

0.271

Asia WGS

AF:

0.247

AC:

860

AN:

3478

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

-0.58

CADD

Benign

7.7

DANN

Benign

0.69

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