rs1043595

Variant names:

• chr7-128769958-G-A
• rs1043595
• NM_001219.5:c.*791G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-128769958-G-A
• chr7-128769958-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 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=-0.63).
• 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 rank	MANE	Protein	UniProt
CALU	NM_001219.5	c.*791G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000249364.9	NP_001210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALU	ENST00000249364.9	c.*791G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_001219.5	ENSP00000249364.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.224 AC: 22 AN: 98

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.0531 AC: 2205 AN: 41530

American (AMR) AF: 0.182 AC: 2777 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 841 AN: 3466

East Asian (EAS) AF: 0.0668 AC: 346 AN: 5180

South Asian (SAS) AF: 0.0764 AC: 368 AN: 4818

European-Finnish (FIN) AF: 0.214 AC: 2260 AN: 10578

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18654 AN: 67988

Other (OTH) AF: 0.200 AC: 422 AN: 2110

Alfa AF: 0.251 Hom.: 10122

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
PhyloP100		0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs1043595; hg19: chr7-128410012;