Variant rs3835190 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_002465.4(MYBPC1):c.1634-18del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 1,610,676 control chromosomes in the GnomAD database, including 57,525 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 3990 hom., cov: 25)

Exomes 𝑓: 0.27 ( 53535 hom. )

Consequence

MYBPC1
NM_002465.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.895

Variant links:

Genes affected

MYBPC1 (HGNC:7549): (myosin binding protein C1) This gene encodes a member of the myosin-binding protein C family. Myosin-binding protein C family members are myosin-associated proteins found in the cross-bridge-bearing zone (C region) of A bands in striated muscle. The encoded protein is the slow skeletal muscle isoform of myosin-binding protein C and plays an important role in muscle contraction by recruiting muscle-type creatine kinase to myosin filaments. Mutations in this gene are associated with distal arthrogryposis type I. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

MYBPC1 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-101653096-AC-A is Benign according to our data. Variant chr12-101653096-AC-A is described in ClinVar as [Benign]. Clinvar id is 258658.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-101653096-AC-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYBPC1	NM_002465.4 linkuse as main transcript	c.1634-18del		intron_variant		ENST00000361466.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYBPC1	ENST00000361466.7 linkuse as main transcript	c.1634-18del		intron_variant		1	NM_002465.4	A2	Q00872-4
	ENST00000547027.1 linkuse as main transcript	n.258-6069del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33631

AN:

151974

Hom.:

3992

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.305

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.232

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.229

GnomAD3 exomes

AF:

0.224

AC:

56156

AN:

250220

Hom.:

7003

AF XY:

0.231

AC XY:

31254

AN XY:

135320

show subpopulations

Gnomad AFR exome

AF:

0.140

Gnomad AMR exome

AF:

0.140

Gnomad ASJ exome

AF:

0.301

Gnomad EAS exome

AF:

0.0792

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.238

Gnomad NFE exome

AF:

0.275

Gnomad OTH exome

AF:

0.248

GnomAD4 exome

AF:

0.265

AC:

386654

AN:

1458584

Hom.:

53535

Cov.:

AF XY:

0.265

AC XY:

192262

AN XY:

725802

show subpopulations

Gnomad4 AFR exome

AF:

0.143

Gnomad4 AMR exome

AF:

0.144

Gnomad4 ASJ exome

AF:

0.301

Gnomad4 EAS exome

AF:

0.0890

Gnomad4 SAS exome

AF:

0.229

Gnomad4 FIN exome

AF:

0.240

Gnomad4 NFE exome

AF:

0.283

Gnomad4 OTH exome

AF:

0.259

GnomAD4 genome

AF:

0.221

AC:

33627

AN:

152092

Hom.:

3990

Cov.:

AF XY:

0.217

AC XY:

16157

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.144

Gnomad4 AMR

AF:

0.189

Gnomad4 ASJ

AF:

0.305

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.223

Gnomad4 FIN

AF:

0.232

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.229

Alfa

AF:

0.190

Hom.:

620

Bravo

AF:

0.211

Asia WGS

AF:

0.155

AC:

541

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Myopathy, congenital, with tremor

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Lethal congenital contracture syndrome 4

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 10, 2018

- -

Arthrogryposis, distal, type 1B

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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