17-12738949-TTA-T

Variant summary

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

The NM_001146312.3(MYOCD):c.592-242_592-241del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.60 (26876 hom., cov: 0)
• Consequence: MYOCD NM_001146312.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.675

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 17-12738949-TTA-T is Benign according to our data. Variant chr17-12738949-TTA-T is described in ClinVar as [Benign]. Clinvar id is 1262861.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYOCD	NM_001146312.3	c.592-242_592-241del		intron_variant		ENST00000425538.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYOCD	ENST00000425538.6	c.592-242_592-241del		intron_variant		1	NM_001146312.3	P2
MYOCD	ENST00000343344.8	c.592-242_592-241del		intron_variant		1		A2
MYOCD	ENST00000395988.1	n.512-242_512-241del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90043 AN: 151076 Hom.: 26833 Cov.: 0

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.596 AC: 90141 AN: 151186 Hom.: 26876 Cov.: 0 AF XY: 0.596 AC XY: 44018 AN XY: 73828

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.573

Bravo AF: 0.593

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

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs35061930; hg19: chr17-12642266;