rs1548349
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_024919.6(FRMD1):c.1366C>T(p.Gln456*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000697 in 1,434,706 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
FRMD1
NM_024919.6 stop_gained
NM_024919.6 stop_gained
Scores
2
2
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.09
Publications
19 publications found
Genes affected
FRMD1 (HGNC:21240): (FERM domain containing 1) Predicted to be involved in positive regulation of hippo signaling. Predicted to be located in cytoskeleton. Predicted to be active in cytoplasmic side of apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FRMD1 | NM_024919.6 | c.1366C>T | p.Gln456* | stop_gained | Exon 10 of 11 | ENST00000283309.11 | NP_079195.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FRMD1 | ENST00000283309.11 | c.1366C>T | p.Gln456* | stop_gained | Exon 10 of 11 | 1 | NM_024919.6 | ENSP00000283309.6 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.97e-7 AC: 1AN: 1434706Hom.: 0 Cov.: 51 AF XY: 0.00000141 AC XY: 1AN XY: 711746 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1434706
Hom.:
Cov.:
51
AF XY:
AC XY:
1
AN XY:
711746
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
33262
American (AMR)
AF:
AC:
0
AN:
41898
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25744
East Asian (EAS)
AF:
AC:
0
AN:
38840
South Asian (SAS)
AF:
AC:
0
AN:
82632
European-Finnish (FIN)
AF:
AC:
1
AN:
45260
Middle Eastern (MID)
AF:
AC:
0
AN:
5266
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1102330
Other (OTH)
AF:
AC:
0
AN:
59474
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.275
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
DANN
Benign
DEOGEN2
Benign
.;.;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;.;.;.;.
MetaRNN
Benign
.;.;.;.;.
MutationAssessor
Benign
.;.;.;.;.
PhyloP100
PROVEAN
Benign
.;.;.;.;.
REVEL
Benign
Sift
Pathogenic
.;.;.;.;.
Sift4G
Pathogenic
.;.;.;.;.
Vest4
GERP RS
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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