rs13059488
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The ENST00000398540.8(FRMD4B):āc.991T>Cā(p.Leu331=) variant causes a synonymous change. The variant allele was found at a frequency of 0.911 in 1,607,080 control chromosomes in the GnomAD database, including 675,649 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: š 0.82 ( 53705 hom., cov: 32)
Exomes š: 0.92 ( 621944 hom. )
Consequence
FRMD4B
ENST00000398540.8 synonymous
ENST00000398540.8 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.79
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FRMD4B | NM_015123.3 | c.991T>C | p.Leu331= | synonymous_variant | 13/23 | ENST00000398540.8 | NP_055938.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRMD4B | ENST00000398540.8 | c.991T>C | p.Leu331= | synonymous_variant | 13/23 | 1 | NM_015123.3 | ENSP00000381549 | P1 |
Frequencies
GnomAD3 genomes AF: 0.822 AC: 124981AN: 152082Hom.: 53689 Cov.: 32
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GnomAD3 exomes AF: 0.881 AC: 218908AN: 248548Hom.: 98327 AF XY: 0.883 AC XY: 119078AN XY: 134858
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GnomAD4 exome AF: 0.920 AC: 1339192AN: 1454880Hom.: 621944 Cov.: 29 AF XY: 0.918 AC XY: 664717AN XY: 724152
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GnomAD4 genome AF: 0.822 AC: 125039AN: 152200Hom.: 53705 Cov.: 32 AF XY: 0.820 AC XY: 61007AN XY: 74414
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Not reported inComputational scores
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Benign
CADD
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DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at