rs2383156
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001375567.1(FOCAD):c.2625+11G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,467,584 control chromosomes in the GnomAD database, including 248,967 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.59 ( 26281 hom., cov: 31)
Exomes 𝑓: 0.58 ( 222686 hom. )
Consequence
FOCAD
NM_001375567.1 intron
NM_001375567.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.797
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
?
Variant 9-20885241-G-A is Benign according to our data. Variant chr9-20885241-G-A is described in ClinVar as [Benign]. Clinvar id is 402872.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-20885241-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOCAD | NM_001375567.1 | c.2625+11G>A | intron_variant | ENST00000338382.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOCAD | ENST00000338382.11 | c.2625+11G>A | intron_variant | 5 | NM_001375567.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.587 AC: 88972AN: 151650Hom.: 26277 Cov.: 31
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GnomAD3 exomes AF: 0.588 AC: 109363AN: 186028Hom.: 32541 AF XY: 0.586 AC XY: 59924AN XY: 102192
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GnomAD4 exome AF: 0.581 AC: 763866AN: 1315816Hom.: 222686 Cov.: 33 AF XY: 0.581 AC XY: 377470AN XY: 649482
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GnomAD4 genome ? AF: 0.586 AC: 89006AN: 151768Hom.: 26281 Cov.: 31 AF XY: 0.588 AC XY: 43639AN XY: 74154
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at