rs11636081
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_015322.5(FEM1B):c.249-1880G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 152,156 control chromosomes in the GnomAD database, including 66 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 0.022 ( 66 hom., cov: 32)
Consequence
FEM1B
NM_015322.5 intron
NM_015322.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.46
Genes affected
FEM1B (HGNC:3649): (fem-1 homolog B) This gene encodes an ankyrin repeat protein that belongs to the death receptor-associated family of proteins and plays a role in mediating apoptosis. The encoded protein is also thought to function in the replication stress-induced checkpoint signaling pathway via interaction with checkpoint kinase 1. [provided by RefSeq, Aug 2013]
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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=-0.83).
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0218 (3313/152156) while in subpopulation AMR AF= 0.0325 (498/15300). AF 95% confidence interval is 0.0302. There are 66 homozygotes in gnomad4. There are 1651 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 66 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FEM1B | NM_015322.5 | c.249-1880G>A | intron_variant | ENST00000306917.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FEM1B | ENST00000306917.5 | c.249-1880G>A | intron_variant | 1 | NM_015322.5 | P1 | |||
FEM1B | ENST00000570067.1 | c.-226-1880G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0218 AC: 3314AN: 152042Hom.: 66 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0218 AC: 3313AN: 152156Hom.: 66 Cov.: 32 AF XY: 0.0222 AC XY: 1651AN XY: 74390
GnomAD4 genome
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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