dbSNP rs6834736: CRACD:c.*555C>G (chr4-56328359-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001393381.1(CRACD):c.*555C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 517,996 control chromosomes in the GnomAD database, including 81,629 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 0.56 ( 23978 hom., cov: 32)

Exomes 𝑓: 0.56 ( 57651 hom. )

Consequence

CRACD
NM_001393381.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.972

Publications

10 publications found

Variant links:

Genes affected

CRACD (HGNC:29219): (capping protein inhibiting regulator of actin dynamics) Involved in negative regulation of barbed-end actin filament capping. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

CRACD links:

Genome browser will be placed here

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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRACD	NM_001393381.1 link	c.*555C>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000682029.1	NP_001380310.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
CRACD	ENST00000682029.1 link	c.*555C>G	3_prime_UTR_variant	Exon 11 of 11		NM_001393381.1	ENSP00000507165.1
CRACD	ENST00000264229.11 link	c.*555C>G	3_prime_UTR_variant	Exon 11 of 11	2		ENSP00000264229.6
CRACD	ENST00000504228.6 link	c.*555C>G	3_prime_UTR_variant	Exon 10 of 10	5		ENSP00000423366.1

Frequencies

GnomAD3 genomes

AF:

0.558

AC:

84785

AN:

151830

Hom.:

23965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.582

Gnomad AMI

AF:

0.501

Gnomad AMR

AF:

0.646

Gnomad ASJ

AF:

0.477

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.555

Gnomad FIN

AF:

0.545

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.555

Gnomad OTH

AF:

0.557

GnomAD2 exomes

AF:

0.550

AC:

127160

AN:

231234

AF XY:

0.546

show subpopulations

Gnomad AFR exome

AF:

0.587

Gnomad AMR exome

AF:

0.683

Gnomad ASJ exome

AF:

0.481

Gnomad EAS exome

AF:

0.266

Gnomad FIN exome

AF:

0.553

Gnomad NFE exome

AF:

0.549

Gnomad OTH exome

AF:

0.530

GnomAD4 exome

AF:

0.556

AC:

203419

AN:

366048

Hom.:

57651

Cov.:

AF XY:

0.554

AC XY:

116232

AN XY:

209902

show subpopulations

African (AFR)

AF:

0.584

AC:

6114

AN:

10472

American (AMR)

AF:

0.681

AC:

24659

AN:

36226

Ashkenazi Jewish (ASJ)

AF:

0.480

AC:

5625

AN:

11724

East Asian (EAS)

AF:

0.262

AC:

3442

AN:

13144

South Asian (SAS)

AF:

0.578

AC:

38476

AN:

66586

European-Finnish (FIN)

AF:

0.552

AC:

9332

AN:

16898

Middle Eastern (MID)

AF:

0.527

AC:

1503

AN:

2850

European-Non Finnish (NFE)

AF:

0.550

AC:

105314

AN:

191582

Other (OTH)

AF:

0.541

AC:

8954

AN:

16566

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.431

Heterozygous variant carriers

4437

8874

13312

17749

22186

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

810

1620

2430

3240

4050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.558

AC:

84846

AN:

151948

Hom.:

23978

Cov.:

AF XY:

0.557

AC XY:

41389

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.582

AC:

24092

AN:

41422

American (AMR)

AF:

0.647

AC:

9879

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.477

AC:

1656

AN:

3470

East Asian (EAS)

AF:

0.260

AC:

1341

AN:

5160

South Asian (SAS)

AF:

0.555

AC:

2675

AN:

4816

European-Finnish (FIN)

AF:

0.545

AC:

5750

AN:

10550

Middle Eastern (MID)

AF:

0.531

AC:

155

AN:

292

European-Non Finnish (NFE)

AF:

0.555

AC:

37681

AN:

67946

Other (OTH)

AF:

0.551

AC:

1161

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1940

3879

5819

7758

9698

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<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:

0.544

Hom.:

4151

Bravo

AF:

0.566

Asia WGS

AF:

0.442

AC:

1537

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.0

(source)

DANN

Benign

0.31

PhyloP100

0.97

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over