rs1043550

chr7-128769171-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CALU	NM_001219.5	c.*4A>G		3_prime_UTR_variant	7/7	ENST00000249364.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALU	ENST00000249364.9	c.*4A>G		3_prime_UTR_variant	7/7	1	NM_001219.5

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45617 AN: 151932 Hom.: 8083 Cov.: 31

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

GnomAD3 exomes AF: 0.311 AC: 72201 AN: 232266 Hom.: 12693 AF XY: 0.319 AC XY: 40052 AN XY: 125500

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 SAS exome AF: 0.208

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.: 19 AF XY: 0.368 AC XY: 243756 AN XY: 662748

Gnomad4 AFR exome AF: 0.141

Gnomad4 AMR exome AF: 0.244

Gnomad4 ASJ exome AF: 0.390

Gnomad4 EAS exome AF: 0.0607

Gnomad4 SAS exome AF: 0.211

Gnomad4 FIN exome AF: 0.328

Gnomad4 NFE exome AF: 0.410

Gnomad4 OTH exome AF: 0.346

GnomAD4 genome AF: 0.300 AC: 45619 AN: 152050 Hom.: 8087 Cov.: 31 AF XY: 0.294 AC XY: 21870 AN XY: 74324

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.0685

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.326

Alfa AF: 0.387 Hom.: 26471

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
Dann	Benign	0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

dbSNP: rs1043550; hg19: chr7-128409225; COSMIC: COSV50821391; COSMIC: COSV50821391;