rs339054

Variant names:

• chr7-128742457-T-G
• rs339054
• NM_001219.5:c.-12+3025T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001219.5(CALU):​c.-12+3025T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,128 control chromosomes in the GnomAD database, including 22,424 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 0.53 (22424 hom., cov: 33)
• Consequence: CALU NM_001219.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALU	NM_001219.5	c.-12+3025T>G		intron_variant	Intron 1 of 6	ENST00000249364.9	NP_001210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALU	ENST00000249364.9	c.-12+3025T>G		intron_variant	Intron 1 of 6	1	NM_001219.5	ENSP00000249364.4

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80062 AN: 152010 Hom.: 22380 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.529

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.527 AC: 80165 AN: 152128 Hom.: 22424 Cov.: 33 AF XY: 0.518 AC XY: 38497 AN XY: 74356

African (AFR) AF: 0.704 AC: 29244 AN: 41518

American (AMR) AF: 0.413 AC: 6316 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1815 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1198 AN: 5182

South Asian (SAS) AF: 0.346 AC: 1671 AN: 4830

European-Finnish (FIN) AF: 0.430 AC: 4530 AN: 10538

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.495 AC: 33625 AN: 67996

Other (OTH) AF: 0.528 AC: 1117 AN: 2114

Alfa AF: 0.504 Hom.: 67194

Bravo AF: 0.539

Asia WGS AF: 0.317 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs339054; hg19: chr7-128382511;