rs13072552

chr3-149195339-G-T

Variant summary

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

The NM_000096.4(CP):c.1713+3028C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,154 control chromosomes in the GnomAD database, including 4,215 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 0.17 (4215 hom., cov: 32)
• Consequence: CP NM_000096.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521

Genes affected

CP (HGNC:2295): (ceruloplasmin) The protein encoded by this gene is a metalloprotein that binds most of the copper in plasma and is involved in the peroxidation of Fe(II)transferrin to Fe(III) transferrin. Mutations in this gene cause aceruloplasminemia, which results in iron accumulation and tissue damage, and is associated with diabetes and neurologic abnormalities. Two transcript variants, one protein-coding and the other not protein-coding, have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CP	NM_000096.4	c.1713+3028C>A		intron_variant		ENST00000264613.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CP	ENST00000264613.11	c.1713+3028C>A		intron_variant		1	NM_000096.4	P1

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25707 AN: 152040 Hom.: 4200 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0334

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0778

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.169 AC: 25767 AN: 152154 Hom.: 4215 Cov.: 32 AF XY: 0.165 AC XY: 12267 AN XY: 74394

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.0903

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0328

Gnomad4 FIN AF: 0.0510

Gnomad4 NFE AF: 0.0778

Gnomad4 OTH AF: 0.150

Alfa AF: 0.0908 Hom.: 1338

Bravo AF: 0.184

Asia WGS AF: 0.0510 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.60
Dann	Benign	0.63

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: rs13072552; hg19: chr3-148913126;