12-8222185-C-CACG
Variant names:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1
The NM_018088.3(FAM90A1):c.1031_1032insCGT(p.Thr344_Ser345insVal) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.53 ( 23703 hom., cov: 0)
Exomes 𝑓: 0.68 ( 326290 hom. )
Failed GnomAD Quality Control
Consequence
FAM90A1
NM_018088.3 disruptive_inframe_insertion
NM_018088.3 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -3.63
Genes affected
FAM90A1 (HGNC:25526): (family with sequence similarity 90 member A1) FAM90A1 belongs to subfamily I of the primate-specific FAM90A gene family, which originated from multiple duplications and rearrangements (Bosch et al., 2007 [PubMed 17684299]).[supplied by OMIM, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_018088.3. Strenght limited to Supporting due to length of the change: 1aa.
BP6
Variant 12-8222185-C-CACG is Benign according to our data. Variant chr12-8222185-C-CACG is described in ClinVar as [Benign]. Clinvar id is 768513.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM90A1 | ENST00000538603.6 | c.1031_1032insCGT | p.Thr344_Ser345insVal | disruptive_inframe_insertion | Exon 7 of 7 | 1 | NM_018088.3 | ENSP00000445418.1 | ||
FAM90A1 | ENST00000307435.10 | c.1031_1032insCGT | p.Thr344_Ser345insVal | disruptive_inframe_insertion | Exon 6 of 6 | 2 | ENSP00000307798.6 |
Frequencies
GnomAD3 genomes AF: 0.526 AC: 79918AN: 151812Hom.: 23709 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.677 AC: 987221AN: 1459264Hom.: 326290 Cov.: 80 AF XY: 0.672 AC XY: 488091AN XY: 725930
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.526 AC: 79903AN: 151930Hom.: 23703 Cov.: 0 AF XY: 0.522 AC XY: 38747AN XY: 74242
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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
Aug 09, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at