17-12715310-C-CCT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001146312.3(MYOCD):c.122-209_122-208insCT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.71 (39006 hom., cov: 0)
• Consequence: MYOCD NM_001146312.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.115

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-12715310-C-CCT is Benign according to our data. Variant chr17-12715310-C-CCT is described in ClinVar as [Benign]. Clinvar id is 1222172.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYOCD	NM_001146312.3	c.122-209_122-208insCT		intron_variant		ENST00000425538.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYOCD	ENST00000425538.6	c.122-209_122-208insCT		intron_variant		1	NM_001146312.3	P2
MYOCD	ENST00000343344.8	c.122-209_122-208insCT		intron_variant		1		A2
MYOCD	ENST00000579237.5	c.*40-209_*40-208insCT		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108222 AN: 151640 Hom.: 38968 Cov.: 0

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.710

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.714 AC: 108314 AN: 151758 Hom.: 39006 Cov.: 0 AF XY: 0.714 AC XY: 52943 AN XY: 74142

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.709

Alfa AF: 0.714 Hom.: 2456

Bravo AF: 0.704

Asia WGS AF: 0.618 AC: 2153 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16713; hg19: chr17-12618627;