Variant chr17-12717444-A-G 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_001146312.3(MYOCD):c.253+23A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 1,587,076 control chromosomes in the GnomAD database, including 467,080 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.74 ( 41997 hom., cov: 32)

Exomes 𝑓: 0.77 ( 425083 hom. )

Consequence

MYOCD
NM_001146312.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.922

Variant links:

Genes affected

MYOCD (HGNC:16067): (myocardin) This gene encodes a nuclear protein, which is expressed in heart, aorta, and in smooth muscle cell-containing tissues. It functions as a transcriptional co-activator of serum response factor (SRF) and modulates expression of cardiac and smooth muscle-specific SRF-target genes, and thus may play a crucial role in cardiogenesis and differentiation of the smooth muscle cell lineage. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

MYOCD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 17-12717444-A-G is Benign according to our data. Variant chr17-12717444-A-G is described in ClinVar as [Benign]. Clinvar id is 1225489.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYOCD	NM_001146312.3 linkuse as main transcript	c.253+23A>G		intron_variant		ENST00000425538.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYOCD	ENST00000425538.6 linkuse as main transcript	c.253+23A>G		intron_variant		1	NM_001146312.3	P2	Q8IZQ8-3
MYOCD	ENST00000343344.8 linkuse as main transcript	c.253+23A>G		intron_variant		1		A2	Q8IZQ8-1

Frequencies

GnomAD3 genomes

AF:

0.740

AC:

112405

AN:

151944

Hom.:

41962

Cov.:

show subpopulations

Gnomad AFR

AF:

0.705

Gnomad AMI

AF:

0.716

Gnomad AMR

AF:

0.631

Gnomad ASJ

AF:

0.732

Gnomad EAS

AF:

0.709

Gnomad SAS

AF:

0.689

Gnomad FIN

AF:

0.770

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.788

Gnomad OTH

AF:

0.737

GnomAD3 exomes

AF:

0.727

AC:

179778

AN:

247210

Hom.:

66137

AF XY:

0.732

AC XY:

97650

AN XY:

133420

show subpopulations

Gnomad AFR exome

AF:

0.701

Gnomad AMR exome

AF:

0.563

Gnomad ASJ exome

AF:

0.720

Gnomad EAS exome

AF:

0.710

Gnomad SAS exome

AF:

0.692

Gnomad FIN exome

AF:

0.775

Gnomad NFE exome

AF:

0.784

Gnomad OTH exome

AF:

0.736

GnomAD4 exome

AF:

0.768

AC:

1101703

AN:

1435014

Hom.:

425083

Cov.:

AF XY:

0.766

AC XY:

547802

AN XY:

715170

show subpopulations

Gnomad4 AFR exome

AF:

0.698

Gnomad4 AMR exome

AF:

0.564

Gnomad4 ASJ exome

AF:

0.720

Gnomad4 EAS exome

AF:

0.723

Gnomad4 SAS exome

AF:

0.689

Gnomad4 FIN exome

AF:

0.781

Gnomad4 NFE exome

AF:

0.787

Gnomad4 OTH exome

AF:

0.762

GnomAD4 genome

AF:

0.740

AC:

112482

AN:

152062

Hom.:

41997

Cov.:

AF XY:

0.735

AC XY:

54611

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.705

Gnomad4 AMR

AF:

0.630

Gnomad4 ASJ

AF:

0.732

Gnomad4 EAS

AF:

0.709

Gnomad4 SAS

AF:

0.689

Gnomad4 FIN

AF:

0.770

Gnomad4 NFE

AF:

0.788

Gnomad4 OTH

AF:

0.735

Alfa

AF:

0.763

Hom.:

75572

Bravo

AF:

0.727

Asia WGS

AF:

0.699

AC:

2436

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	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.063

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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