chr16-23608057-T-C
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_024675.4(PALB2):c.3202-45A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000208 in 1,587,370 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
Consequence
NM_024675.4 intron
Scores
Clinical Significance
Conservation
Publications
- hereditary breast carcinomaInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen, Ambry Genetics
- Fanconi anemia complementation group NInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
- pancreatic cancer, susceptibility to, 3Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
- familial ovarian cancerInheritance: AD Classification: MODERATE Submitted by: ClinGen
- Fanconi anemiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- hereditary nonpolyposis colon cancerInheritance: AD Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151826Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000243 AC: 6AN: 246982 AF XY: 0.0000149 show subpopulations
GnomAD4 exome AF: 0.0000209 AC: 30AN: 1435544Hom.: 0 Cov.: 28 AF XY: 0.0000238 AC XY: 17AN XY: 715582 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151826Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74142 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Familial cancer of breast Benign:1
Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitter to LOVD: Marc Tischkowitz. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at