rs4075188
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015123.3(FRMD4B):c.877-6195C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0887 in 148,484 control chromosomes in the GnomAD database, including 576 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 0.089 ( 576 hom., cov: 30)
Consequence
FRMD4B
NM_015123.3 intron
NM_015123.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.63
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0966 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRMD4B | NM_015123.3 | c.877-6195C>T | intron_variant | ENST00000398540.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRMD4B | ENST00000398540.8 | c.877-6195C>T | intron_variant | 1 | NM_015123.3 | P1 | |||
FRMD4B | ENST00000470070.6 | n.771-6195C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
FRMD4B | ENST00000483668.5 | n.489-6195C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
FRMD4B | ENST00000487751.1 | n.502-6195C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0887 AC: 13164AN: 148380Hom.: 575 Cov.: 30
GnomAD3 genomes
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13164
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0887 AC: 13176AN: 148484Hom.: 576 Cov.: 30 AF XY: 0.0862 AC XY: 6216AN XY: 72094
GnomAD4 genome
?
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AC:
13176
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148484
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30
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6216
AN XY:
72094
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90
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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
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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