rs3900770
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_031281.3(FCRL5):c.*767A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0952 in 152,360 control chromosomes in the GnomAD database, including 1,241 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 0.095 ( 1241 hom., cov: 33)
Exomes 𝑓: 0.068 ( 0 hom. )
Consequence
FCRL5
NM_031281.3 3_prime_UTR
NM_031281.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.892
Genes affected
FCRL5 (HGNC:18508): (Fc receptor like 5) This gene encodes a member of the immunoglobulin receptor superfamily and the Fc-receptor like family. This gene and several other Fc receptor-like gene members are clustered on the long arm of chromosome 1. The encoded protein is a single-pass type I membrane protein and contains 8 immunoglobulin-like C2-type domains. This gene is implicated in B cell development and lymphomagenesis. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Sep 2010]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCRL5 | NM_031281.3 | c.*767A>G | 3_prime_UTR_variant | 17/17 | ENST00000361835.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCRL5 | ENST00000361835.8 | c.*767A>G | 3_prime_UTR_variant | 17/17 | 1 | NM_031281.3 | P1 | ||
FCRL5 | ENST00000461387.5 | n.2978A>G | non_coding_transcript_exon_variant | 7/7 | 2 | ||||
FCRL5 | ENST00000462218.1 | n.1089A>G | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
FCRL5 | ENST00000497286.5 | n.2794A>G | non_coding_transcript_exon_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0952 AC: 14486AN: 152110Hom.: 1239 Cov.: 33
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GnomAD4 exome AF: 0.0682 AC: 9AN: 132Hom.: 0 Cov.: 0 AF XY: 0.0897 AC XY: 7AN XY: 78
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GnomAD4 genome ? AF: 0.0952 AC: 14495AN: 152228Hom.: 1241 Cov.: 33 AF XY: 0.0906 AC XY: 6743AN XY: 74440
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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