7-128769958-G-A

Position:

• chr7-128769958-G-A

Variant summary

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

The NM_001219.5(CALU):​c.*791G>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 0.186 in 152,258 control chromosomes in the GnomAD database, including 3,415 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 0.19 (3413 hom., cov: 32)
  • Exomes 𝑓: 0.25 (2 hom.)
• Consequence: CALU NM_001219.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835

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=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALU	NM_001219.5	c.*791G>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.*791G>A		3_prime_UTR_variant	7/7	1	NM_001219.5

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28345 AN: 152038 Hom.: 3412 Cov.: 32

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.202

GnomAD4 exome AF: 0.245 AC: 25 AN: 102 Hom.: 2 Cov.: 0 AF XY: 0.257 AC XY: 18 AN XY: 70

Gnomad4 FIN exome AF: 0.224

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.186 AC: 28341 AN: 152156 Hom.: 3413 Cov.: 32 AF XY: 0.182 AC XY: 13565 AN XY: 74356

Gnomad4 AFR AF: 0.0531

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.0668

Gnomad4 SAS AF: 0.0764

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.200

Alfa AF: 0.256 Hom.: 7538

Bravo AF: 0.183

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.74
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1043595; hg19: chr7-128410012;