dbSNP rs1043550: CALU:c.*4A>G (chr7-128769171-A-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_001219.5(CALU):c.*4A>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 0.363 in 1,472,348 control chromosomes in the GnomAD database, including 104,308 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 0.30 ( 8087 hom., cov: 31)

Exomes 𝑓: 0.37 ( 96221 hom. )

Consequence

CALU
NM_001219.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0390

Publications

35 publications found

Variant links:

Genes affected

CALU (HGNC:1458): (calumenin) The product of this gene is a calcium-binding protein localized in the endoplasmic reticulum (ER) and it is involved in such ER functions as protein folding and sorting. This protein belongs to a family of multiple EF-hand proteins (CERC) that include reticulocalbin, ERC-55, and Cab45 and the product of this gene. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2008]

CALU 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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALU	NM_001219.5 link	c.*4A>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000249364.9	NP_001210.1	O43852-1Q6IAW5B3KQF5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALU	ENST00000249364.9 link	c.*4A>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_001219.5	ENSP00000249364.4		O43852-1

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45617

AN:

151932

Hom.:

8083

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.531

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.394

Gnomad EAS

AF:

0.0678

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.335

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.411

Gnomad OTH

AF:

0.330

GnomAD2 exomes

AF:

0.311

AC:

72201

AN:

232266

AF XY:

0.319

show subpopulations

Gnomad AFR exome

AF:

0.143

Gnomad AMR exome

AF:

0.241

Gnomad ASJ exome

AF:

0.393

Gnomad EAS exome

AF:

0.0578

Gnomad FIN exome

AF:

0.325

Gnomad NFE exome

AF:

0.407

Gnomad OTH exome

AF:

0.356

GnomAD4 exome

AF:

0.370

AC:

488908

AN:

1320298

Hom.:

96221

Cov.:

AF XY:

0.368

AC XY:

243756

AN XY:

662748

show subpopulations

African (AFR)

AF:

0.141

AC:

4244

AN:

30196

American (AMR)

AF:

0.244

AC:

9460

AN:

38798

Ashkenazi Jewish (ASJ)

AF:

0.390

AC:

9536

AN:

24470

East Asian (EAS)

AF:

0.0607

AC:

2365

AN:

38962

South Asian (SAS)

AF:

0.211

AC:

16809

AN:

79478

European-Finnish (FIN)

AF:

0.328

AC:

17380

AN:

53026

Middle Eastern (MID)

AF:

0.393

AC:

2151

AN:

5476

European-Non Finnish (NFE)

AF:

0.410

AC:

407674

AN:

994194

Other (OTH)

AF:

0.346

AC:

19289

AN:

55698

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

12547

25094

37642

50189

62736

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11692

23384

35076

46768

58460

<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:

0.300

AC:

45619

AN:

152050

Hom.:

8087

Cov.:

AF XY:

0.294

AC XY:

21870

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.148

AC:

6137

AN:

41460

American (AMR)

AF:

0.268

AC:

4089

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.394

AC:

1369

AN:

3472

East Asian (EAS)

AF:

0.0685

AC:

355

AN:

5182

South Asian (SAS)

AF:

0.199

AC:

960

AN:

4822

European-Finnish (FIN)

AF:

0.335

AC:

3536

AN:

10562

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.410

AC:

27890

AN:

67952

Other (OTH)

AF:

0.326

AC:

688

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1461

2922

4383

5844

7305

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.374

Hom.:

48347

Bravo

AF:

0.293

Asia WGS

AF:

0.128

AC:

444

AN:

3478

EpiCase

AF:

0.423

EpiControl

AF:

0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.7

(source)

DANN

Benign

0.49

PhyloP100

0.039

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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