rs758187

Variant names:

• chr17-12665754-T-C
• rs758187
• NM_001146312.3:c.-435T>C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001146312.3(MYOCD):​c.-435T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 158,126 control chromosomes in the GnomAD database, including 13,770 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.38 (13574 hom., cov: 33)
  • Exomes 𝑓: 0.23 (196 hom.)
• Consequence: MYOCD NM_001146312.3 upstream_gene
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.664

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 17-12665754-T-C is Benign according to our data. Variant chr17-12665754-T-C is described in ClinVar as [Benign]. Clinvar id is 1253022.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYOCD	NM_001146312.3	c.-435T>C		upstream_gene_variant		ENST00000425538.6	NP_001139784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYOCD	ENST00000425538.6	c.-435T>C		upstream_gene_variant		1	NM_001146312.3	ENSP00000401678.1
MYOCD	ENST00000579237.5	n.-435T>C		upstream_gene_variant		4		ENSP00000462694.1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57738 AN: 152024 Hom.: 13526 Cov.: 33

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.353

GnomAD4 exome AF: 0.232 AC: 1391 AN: 5984 Hom.: 196 AF XY: 0.229 AC XY: 692 AN XY: 3020

Gnomad4 AFR exome AF: 0.629

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.226

Gnomad4 EAS exome AF: 0.190

Gnomad4 SAS exome AF: 0.217

Gnomad4 FIN exome AF: 0.203

Gnomad4 NFE exome AF: 0.210

Gnomad4 OTH exome AF: 0.231

GnomAD4 genome AF: 0.380 AC: 57847 AN: 152142 Hom.: 13574 Cov.: 33 AF XY: 0.378 AC XY: 28125 AN XY: 74370

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.350

Alfa AF: 0.317 Hom.: 1257

Bravo AF: 0.403

Asia WGS AF: 0.229 AC: 799 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 18028454) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs758187; hg19: chr17-12569071;