rs16861598
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000096.4(CP):c.2426-126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0379 in 1,049,508 control chromosomes in the GnomAD database, including 5,872 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 3708 hom., cov: 31)
Exomes 𝑓: 0.023 ( 2164 hom. )
Consequence
CP
NM_000096.4 intron
NM_000096.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.767
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 3-149182259-C-T is Benign according to our data. Variant chr3-149182259-C-T is described in ClinVar as [Benign]. Clinvar id is 1268348.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CP | NM_000096.4 | c.2426-126G>A | intron_variant | ENST00000264613.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CP | ENST00000264613.11 | c.2426-126G>A | intron_variant | 1 | NM_000096.4 | P1 | |||
CP | ENST00000494544.1 | c.1775-126G>A | intron_variant | 1 | |||||
CP | ENST00000490639.5 | n.2458-126G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
CP | ENST00000481169.5 | c.2213-126G>A | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.128 AC: 19402AN: 152020Hom.: 3695 Cov.: 31
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GnomAD4 exome AF: 0.0226 AC: 20279AN: 897372Hom.: 2164 AF XY: 0.0205 AC XY: 9536AN XY: 464422
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GnomAD4 genome ? AF: 0.128 AC: 19464AN: 152136Hom.: 3708 Cov.: 31 AF XY: 0.124 AC XY: 9201AN XY: 74408
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at