Variant chr17-12760860-T-C 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.2389+153T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 644,886 control chromosomes in the GnomAD database, including 30,324 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5623 hom., cov: 32)

Exomes 𝑓: 0.31 ( 24701 hom. )

Consequence

MYOCD
NM_001146312.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.11

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:

ARHGAP44-AS1 (HGNC:):

ARHGAP44-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 17-12760860-T-C is Benign according to our data. Variant chr17-12760860-T-C is described in ClinVar as [Benign]. Clinvar id is 1279478.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYOCD	NM_001146312.3 linkuse as main transcript	c.2389+153T>C		intron_variant		ENST00000425538.6	NP_001139784.1	Q8IZQ8-3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MYOCD	ENST00000425538.6 linkuse as main transcript	c.2389+153T>C	intron_variant		1	NM_001146312.3	ENSP00000401678.1	Q8IZQ8-3
MYOCD	ENST00000343344.8 linkuse as main transcript	c.2245+153T>C	intron_variant		1		ENSP00000341835.4	Q8IZQ8-1
MYOCD	ENST00000443061.1 linkuse as main transcript	c.1375+153T>C	intron_variant		1		ENSP00000400148.2	Q6N065
ARHGAP44-AS1	ENST00000584772.1 linkuse as main transcript	n.2959A>G	non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37420

AN:

152020

Hom.:

5617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0835

Gnomad AMI

AF:

0.395

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.391

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.372

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.259

GnomAD4 exome

AF:

0.309

AC:

152447

AN:

492748

Hom.:

24701

Cov.:

AF XY:

0.308

AC XY:

80020

AN XY:

259848

show subpopulations

Gnomad4 AFR exome

AF:

0.0904

Gnomad4 AMR exome

AF:

0.262

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.379

Gnomad4 SAS exome

AF:

0.271

Gnomad4 FIN exome

AF:

0.370

Gnomad4 NFE exome

AF:

0.321

Gnomad4 OTH exome

AF:

0.288

GnomAD4 genome

AF:

0.246

AC:

37438

AN:

152138

Hom.:

5623

Cov.:

AF XY:

0.249

AC XY:

18501

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0839

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.237

Gnomad4 EAS

AF:

0.392

Gnomad4 SAS

AF:

0.251

Gnomad4 FIN

AF:

0.372

Gnomad4 NFE

AF:

0.319

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.299

Hom.:

14567

Bravo

AF:

0.229

Asia WGS

AF:

0.300

AC:

1043

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	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.073

DANN

Benign

0.68

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