rs515726121
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_024675.4(PALB2):c.49-54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00062 in 1,448,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00065 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00062 ( 0 hom. )
Consequence
PALB2
NM_024675.4 intron
NM_024675.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.05
Genes affected
PALB2 (HGNC:26144): (partner and localizer of BRCA2) This gene encodes a protein that may function in tumor suppression. This protein binds to and colocalizes with the breast cancer 2 early onset protein (BRCA2) in nuclear foci and likely permits the stable intranuclear localization and accumulation of BRCA2. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 16-23638183-G-A is Benign according to our data. Variant chr16-23638183-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 126753.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PALB2 | NM_024675.4 | c.49-54C>T | intron_variant | ENST00000261584.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PALB2 | ENST00000261584.9 | c.49-54C>T | intron_variant | 1 | NM_024675.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000651 AC: 99AN: 152150Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000617 AC: 800AN: 1296694Hom.: 0 AF XY: 0.000604 AC XY: 395AN XY: 654124
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GnomAD4 genome ? AF: 0.000650 AC: 99AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000645 AC XY: 48AN XY: 74450
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Familial cancer of breast Benign:1
Likely benign, no assertion criteria provided | curation | Leiden Open Variation Database | May 13, 2019 | Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitter to LOVD: Marc Tischkowitz. - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at