rs746601138
Your query was ambiguous. Multiple possible variants found:
- chrX-12706923-CTTTTTTTTT-C
- chrX-12706923-CTTTTTTTTT-CTT
- chrX-12706923-CTTTTTTTTT-CTTT
- chrX-12706923-CTTTTTTTTT-CTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTTT
- chrX-12706923-CTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTTTT
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2
The NM_001368397.1(FRMPD4):c.1287+18_1287+26delTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000181 in 609,242 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000024 ( 0 hom., 2 hem., cov: 10)
Exomes 𝑓: 0.000017 ( 0 hom. 3 hem. )
Consequence
FRMPD4
NM_001368397.1 intron
NM_001368397.1 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.48
Publications
1 publications found
Genes affected
FRMPD4 (HGNC:29007): (FERM and PDZ domain containing 4) This gene encodes a multi-domain (WW, PDZ, FERM) containing protein. Through its interaction with other proteins (such as PSD-95), it functions as a positive regulator of dendritic spine morphogenesis and density, and is required for the maintenance of excitatory synaptic transmission. [provided by RefSeq, Jan 2010]
FRMPD4 Gene-Disease associations (from GenCC):
- X-linked complex neurodevelopmental disorderInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- intellectual disability, X-linked 104Inheritance: XL Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Illumina
- non-syndromic X-linked intellectual disabilityInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BS2
High Hemizygotes in GnomAd4 at 2 XL gene
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FRMPD4 | NM_001368397.1 | c.1287+18_1287+26delTTTTTTTTT | intron_variant | Intron 12 of 16 | ENST00000675598.1 | NP_001355326.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FRMPD4 | ENST00000675598.1 | c.1287+9_1287+17delTTTTTTTTT | intron_variant | Intron 12 of 16 | NM_001368397.1 | ENSP00000502607.1 |
Frequencies
GnomAD3 genomes 0.0000243 AC: 2AN: 82297Hom.: 0 Cov.: 10 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
82297
Hom.:
Cov.:
10
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:
GnomAD4 exome AF: 0.0000171 AC: 9AN: 526960Hom.: 0 AF XY: 0.0000194 AC XY: 3AN XY: 154452 show subpopulations
GnomAD4 exome
AF:
AC:
9
AN:
526960
Hom.:
AF XY:
AC XY:
3
AN XY:
154452
show subpopulations
African (AFR)
AF:
AC:
0
AN:
13072
American (AMR)
AF:
AC:
8
AN:
19406
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12513
East Asian (EAS)
AF:
AC:
0
AN:
24564
South Asian (SAS)
AF:
AC:
0
AN:
28175
European-Finnish (FIN)
AF:
AC:
0
AN:
31247
Middle Eastern (MID)
AF:
AC:
0
AN:
2123
European-Non Finnish (NFE)
AF:
AC:
1
AN:
370156
Other (OTH)
AF:
AC:
0
AN:
25704
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.517
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000243 AC: 2AN: 82282Hom.: 0 Cov.: 10 AF XY: 0.000115 AC XY: 2AN XY: 17456 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
82282
Hom.:
Cov.:
10
AF XY:
AC XY:
2
AN XY:
17456
show subpopulations
African (AFR)
AF:
AC:
0
AN:
22378
American (AMR)
AF:
AC:
2
AN:
7120
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2112
East Asian (EAS)
AF:
AC:
0
AN:
2616
South Asian (SAS)
AF:
AC:
0
AN:
1536
European-Finnish (FIN)
AF:
AC:
0
AN:
2172
Middle Eastern (MID)
AF:
AC:
0
AN:
162
European-Non Finnish (NFE)
AF:
AC:
0
AN:
42548
Other (OTH)
AF:
AC:
0
AN:
1079
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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