rs2064068
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017911.4(FAM118A):c.*199C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 613,240 control chromosomes in the GnomAD database, including 73,072 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.40 ( 14619 hom., cov: 31)
Exomes 𝑓: 0.49 ( 58453 hom. )
Consequence
FAM118A
NM_017911.4 3_prime_UTR
NM_017911.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.38
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM118A | NM_017911.4 | c.*199C>T | 3_prime_UTR_variant | 9/9 | ENST00000441876.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM118A | ENST00000441876.7 | c.*199C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_017911.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.397 AC: 60250AN: 151828Hom.: 14619 Cov.: 31
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GnomAD4 exome AF: 0.492 AC: 227026AN: 461294Hom.: 58453 Cov.: 5 AF XY: 0.490 AC XY: 119666AN XY: 244182
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GnomAD4 genome ? AF: 0.397 AC: 60256AN: 151946Hom.: 14619 Cov.: 31 AF XY: 0.391 AC XY: 29055AN XY: 74280
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ClinVar
Not reported inComputational scores
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Name
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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