rs13005
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_018027.5(FRMD4A):c.*3272C>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.56 in 152,516 control chromosomes in the GnomAD database, including 24,321 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 0.56 ( 24236 hom., cov: 33)
Exomes 𝑓: 0.64 ( 85 hom. )
Consequence
FRMD4A
NM_018027.5 3_prime_UTR
NM_018027.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.60
Genes affected
FRMD4A (HGNC:25491): (FERM domain containing 4A) This gene encodes a FERM domain-containing protein that regulates epithelial cell polarity. It connects ADP ribosylation factor 6 (ARF6) with the Par protein complex, which regulates the remodeling of adherens junctions and linear actin cable formation during epithelial cell polarization. Polymorphisms in this gene are associated with Alzheimer's disease, and also with nicotine dependence. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
PRPF18 (HGNC:17351): (pre-mRNA processing factor 18) Pre-mRNA splicing occurs in 2 sequential transesterification steps. The protein encoded by this gene is found to be essential for the catalytic step II in pre-mRNA splicing process. It is found in the spliceosome, and contains seven WD repeats, which function in protein-protein interactions. This protein has a sequence similarity to the yeast splicing factor Prp18. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRMD4A | NM_018027.5 | c.*3272C>T | 3_prime_UTR_variant | 25/25 | ENST00000357447.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRMD4A | ENST00000357447.7 | c.*3272C>T | 3_prime_UTR_variant | 25/25 | 1 | NM_018027.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.560 AC: 85110AN: 151968Hom.: 24214 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.637 AC: 274AN: 430Hom.: 85 Cov.: 0 AF XY: 0.658 AC XY: 171AN XY: 260
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GnomAD4 genome ? AF: 0.560 AC: 85164AN: 152086Hom.: 24236 Cov.: 33 AF XY: 0.566 AC XY: 42099AN XY: 74336
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ClinVar
Not reported inComputational 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