rs11653

chr7-128769526-T-Achr7-128769526-T-C

Variant summary

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

The NM_001219.5(CALU):c.*359T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 156,418 control chromosomes in the GnomAD database, including 8,400 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 (8142 hom., cov: 32)
  • Exomes 𝑓: 0.32 (258 hom.)
• Consequence: CALU NM_001219.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742

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=-0.93).
• 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.*359T>A		3_prime_UTR_variant	7/7	ENST00000249364.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALU	ENST00000249364.9	c.*359T>A		3_prime_UTR_variant	7/7	1	NM_001219.5

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45904 AN: 152004 Hom.: 8137 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.0702

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.332

GnomAD4 exome AF: 0.319 AC: 1371 AN: 4294 Hom.: 258 Cov.: 0 AF XY: 0.327 AC XY: 725 AN XY: 2214

Gnomad4 AFR exome AF: 0.171

Gnomad4 AMR exome AF: 0.220

Gnomad4 ASJ exome AF: 0.338

Gnomad4 EAS exome AF: 0.0524

Gnomad4 SAS exome AF: 0.212

Gnomad4 FIN exome AF: 0.291

Gnomad4 NFE exome AF: 0.380

Gnomad4 OTH exome AF: 0.282

GnomAD4 genome AF: 0.302 AC: 45906 AN: 152124 Hom.: 8142 Cov.: 32 AF XY: 0.297 AC XY: 22069 AN XY: 74354

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.0710

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.327

Alfa AF: 0.339 Hom.: 1177

Bravo AF: 0.294

Asia WGS AF: 0.151 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.75
Dann	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs11653; hg19: chr7-128409580;