9-93497300-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014612.5(FAM120A):c.805-171C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,120 control chromosomes in the GnomAD database, including 7,032 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.28 ( 7032 hom., cov: 33)
Consequence
FAM120A
NM_014612.5 intron
NM_014612.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.731
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 9-93497300-C-T is Benign according to our data. Variant chr9-93497300-C-T is described in ClinVar as [Benign]. Clinvar id is 1275524.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM120A | NM_014612.5 | c.805-171C>T | intron_variant | ENST00000277165.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM120A | ENST00000277165.11 | c.805-171C>T | intron_variant | 1 | NM_014612.5 | P3 | |||
FAM120A | ENST00000375389.7 | c.805-171C>T | intron_variant | 1 | |||||
FAM120A | ENST00000446420.2 | c.337-171C>T | intron_variant | 5 | |||||
FAM120A | ENST00000698944.1 | c.805-171C>T | intron_variant | A1 |
Frequencies
GnomAD3 genomes AF: 0.280 AC: 42534AN: 152002Hom.: 7033 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.280 AC: 42539AN: 152120Hom.: 7032 Cov.: 33 AF XY: 0.281 AC XY: 20889AN XY: 74342
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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 09, 2018 | - - |
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