rs16861590

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000096.4(CP):​c.2555-637T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0161 in 152,242 control chromosomes in the GnomAD database, including 64 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 0.016 ( 64 hom., cov: 32)

Consequence

CP
NM_000096.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0542 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CPNM_000096.4 linkuse as main transcriptc.2555-637T>C intron_variant ENST00000264613.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CPENST00000264613.11 linkuse as main transcriptc.2555-637T>C intron_variant 1 NM_000096.4 P1
CPENST00000494544.1 linkuse as main transcriptc.1904-637T>C intron_variant 1
CPENST00000490639.5 linkuse as main transcriptn.2587-637T>C intron_variant, non_coding_transcript_variant 1
CPENST00000481169.5 linkuse as main transcriptc.2342-637T>C intron_variant, NMD_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0160
AC:
2441
AN:
152124
Hom.:
61
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0558
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00629
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00766
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0161
AC:
2458
AN:
152242
Hom.:
64
Cov.:
32
AF XY:
0.0155
AC XY:
1152
AN XY:
74434
show subpopulations
Gnomad4 AFR
AF:
0.0561
Gnomad4 AMR
AF:
0.00628
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.00758
Alfa
AF:
0.0134
Hom.:
7
Bravo
AF:
0.0184
Asia WGS
AF:
0.00606
AC:
21
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
9.2
DANN
Benign
0.73

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16861590; hg19: chr3-148898086; API