ENST00000356218.8:c.-147+38525A>C
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000356218.8(FRMD6):c.-147+38525A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,144 control chromosomes in the GnomAD database, including 2,641 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 0.17 ( 2641 hom., cov: 32)
Consequence
FRMD6
ENST00000356218.8 intron
ENST00000356218.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.12
Publications
3 publications found
Genes affected
FRMD6 (HGNC:19839): (FERM domain containing 6) Predicted to be involved in actomyosin structure organization. Predicted to act upstream of or within apical constriction; cellular protein localization; and regulation of actin filament-based process. Predicted to be located in apical junction complex. Predicted to be active in cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FRMD6 | NM_001042481.3 | c.-147+38525A>C | intron_variant | Intron 2 of 14 | NP_001035946.1 | |||
FRMD6 | XM_011536424.2 | c.-147+38525A>C | intron_variant | Intron 3 of 15 | XP_011534726.1 | |||
FRMD6 | XM_024449473.2 | c.-146-80756A>C | intron_variant | Intron 1 of 13 | XP_024305241.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRMD6 | ENST00000356218.8 | c.-147+38525A>C | intron_variant | Intron 2 of 14 | 1 | ENSP00000348550.4 | ||||
FRMD6 | ENST00000554745.1 | n.278-34517A>C | intron_variant | Intron 2 of 2 | 4 | |||||
FRMD6 | ENST00000556137.5 | n.508+38525A>C | intron_variant | Intron 3 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.171 AC: 26035AN: 152026Hom.: 2638 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
26035
AN:
152026
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.171 AC: 26054AN: 152144Hom.: 2641 Cov.: 32 AF XY: 0.173 AC XY: 12847AN XY: 74366 show subpopulations
GnomAD4 genome
AF:
AC:
26054
AN:
152144
Hom.:
Cov.:
32
AF XY:
AC XY:
12847
AN XY:
74366
show subpopulations
African (AFR)
AF:
AC:
2332
AN:
41516
American (AMR)
AF:
AC:
3029
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
429
AN:
3470
East Asian (EAS)
AF:
AC:
790
AN:
5168
South Asian (SAS)
AF:
AC:
834
AN:
4820
European-Finnish (FIN)
AF:
AC:
3034
AN:
10582
Middle Eastern (MID)
AF:
AC:
38
AN:
294
European-Non Finnish (NFE)
AF:
AC:
15110
AN:
67984
Other (OTH)
AF:
AC:
349
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1079
2158
3237
4316
5395
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
284
568
852
1136
1420
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
595
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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