Genetic Variant CSRP3:c.-162delA (chr11-19210493-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000533783.2(CSRP3):c.-162delA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.69 ( 22984 hom., cov: 0)

Exomes 𝑓: 0.50 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CSRP3
ENST00000533783.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:2

Conservation

PhyloP100: 1.16

Publications

1 publications found

Variant links:

Genes affected

CSRP3 (HGNC:2472): (cysteine and glycine rich protein 3) This gene encodes a member of the CSRP family of LIM domain proteins, which may be involved in regulatory processes important for development and cellular differentiation. The LIM/double zinc-finger motif found in this protein is found in a group of proteins with critical functions in gene regulation, cell growth, and somatic differentiation. Mutations in this gene are thought to cause heritable forms of hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) in humans. Alternatively spliced transcript variants with different 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]

CSRP3 links:

CSRP3-AS1 (HGNC:54183): (CSRP3 and E2F8 antisense RNA 1)

CSRP3-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533783.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSRP3-AS1	NR_183675.1		n.207+13593delT		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CSRP3	ENST00000533783.2	TSL:1	c.-162delA	5_prime_UTR	Exon 1 of 7	ENSP00000431813.1	P50461-1
CSRP3-AS1	ENST00000527978.2	TSL:5	n.145+13593delT	intron	N/A
CSRP3-AS1	ENST00000789312.1		n.106+587delT	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.686

AC:

67875

AN:

98948

Hom.:

22996

Cov.:

show subpopulations

Gnomad AFR

AF:

0.463

Gnomad AMI

AF:

0.752

Gnomad AMR

AF:

0.789

Gnomad ASJ

AF:

0.748

Gnomad EAS

AF:

0.803

Gnomad SAS

AF:

0.776

Gnomad FIN

AF:

0.765

Gnomad MID

AF:

0.739

Gnomad NFE

AF:

0.785

Gnomad OTH

AF:

0.705

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.686

AC:

67848

AN:

98926

Hom.:

22984

Cov.:

AF XY:

0.686

AC XY:

32013

AN XY:

46634

show subpopulations

African (AFR)

AF:

0.463

AC:

13754

AN:

29728

American (AMR)

AF:

0.789

AC:

7050

AN:

8940

Ashkenazi Jewish (ASJ)

AF:

0.748

AC:

1824

AN:

2438

East Asian (EAS)

AF:

0.804

AC:

2788

AN:

3468

South Asian (SAS)

AF:

0.776

AC:

2168

AN:

2794

European-Finnish (FIN)

AF:

0.765

AC:

3369

AN:

4406

Middle Eastern (MID)

AF:

0.724

AC:

155

AN:

214

European-Non Finnish (NFE)

AF:

0.785

AC:

35324

AN:

44972

Other (OTH)

AF:

0.705

AC:

938

AN:

1330

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

595

1191

1786

2382

2977

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<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:

0.496

Hom.:

800

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

Dilated Cardiomyopathy, Dominant (1)

Hypertrophic cardiomyopathy (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

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

Publications

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11-19210493-CTTTTTTTTT-CTTTTTTTT

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