dbSNP rs10491102: MYOCD:c.56-18574A>T (chr17-12686554-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001146312.3(MYOCD):c.56-18574A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,190 control chromosomes in the GnomAD database, including 1,002 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1002 hom., cov: 33)

Consequence

MYOCD
NM_001146312.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.543

Publications

1 publications found

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:

MYOCD-AS1 (HGNC:40750): (MYOCD antisense RNA 1)

MYOCD-AS1 links:

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new If you want to explore the variant's impact on the transcript NM_001146312.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001146312.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYOCD	NM_001146312.3	MANE Select	c.56-18574A>T	intron	N/A	NP_001139784.1	Q8IZQ8-3
MYOCD	NM_153604.4		c.56-18574A>T	intron	N/A	NP_705832.1	Q8IZQ8-1
MYOCD	NM_001378306.1		c.-226-18574A>T	intron	N/A	NP_001365235.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYOCD	ENST00000425538.6	TSL:1 MANE Select	c.56-18574A>T	intron	N/A	ENSP00000401678.1	Q8IZQ8-3
MYOCD	ENST00000343344.8	TSL:1	c.56-18574A>T	intron	N/A	ENSP00000341835.4	Q8IZQ8-1
MYOCD-AS1	ENST00000445508.1	TSL:1	n.814-14363T>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16151

AN:

152072

Hom.:

1001

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0636

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.0116

Gnomad SAS

AF:

0.0340

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.103

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

GnomAD4 genome

AF:

0.106

AC:

16168

AN:

152190

Hom.:

1002

Cov.:

AF XY:

0.107

AC XY:

7975

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0636

AC:

2643

AN:

41528

American (AMR)

AF:

0.134

AC:

2050

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

454

AN:

3472

East Asian (EAS)

AF:

0.0116

AC:

AN:

5180

South Asian (SAS)

AF:

0.0338

AC:

163

AN:

4826

European-Finnish (FIN)

AF:

0.181

AC:

1913

AN:

10586

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.126

AC:

8595

AN:

68004

Other (OTH)

AF:

0.103

AC:

217

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

749

1498

2248

2997

3746

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.113

Hom.:

136

Bravo

AF:

0.104

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.7

(source)

DANN

Benign

0.66

PhyloP100

0.54

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over