rs7631421
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000459638.5(FRMD4B):c.-128-25387C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,090 control chromosomes in the GnomAD database, including 9,980 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 0.35 ( 9980 hom., cov: 32)
Consequence
FRMD4B
ENST00000459638.5 intron
ENST00000459638.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0420
Genes affected
FRMD4B (HGNC:24886): (FERM domain containing 4B) This gene encodes a GRP1-binding protein which contains a FERM protein interaction domain as well as two coiled coil domains. This protein may play a role as a scaffolding protein. [provided by RefSeq, Mar 2014]
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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 = 0.456 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRMD4B | XM_017005991.2 | c.-128-25387C>G | intron_variant | ||||
FRMD4B | XM_017005993.2 | c.-128-25387C>G | intron_variant | ||||
FRMD4B | XM_047447767.1 | c.-128-25387C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRMD4B | ENST00000459638.5 | c.-128-25387C>G | intron_variant | 5 | |||||
FRMD4B | ENST00000497880.5 | c.-128-25387C>G | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.354 AC: 53760AN: 151972Hom.: 9972 Cov.: 32
GnomAD3 genomes
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151972
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.354 AC: 53787AN: 152090Hom.: 9980 Cov.: 32 AF XY: 0.351 AC XY: 26088AN XY: 74328
GnomAD4 genome
?
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53787
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152090
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32
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26088
AN XY:
74328
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1192
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at