X-12706923-C-CT
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The NM_001368397.1(FRMPD4):c.1287+26dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.24 ( 2006 hom., 2707 hem., cov: 10)
Exomes 𝑓: 0.098 ( 43 hom. 222 hem. )
Consequence
FRMPD4
NM_001368397.1 intron
NM_001368397.1 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.738
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
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FRMPD4 | NM_001368397.1 | c.1287+26dupT | 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+8_1287+9insT | intron_variant | Intron 12 of 16 | NM_001368397.1 | ENSP00000502607.1 |
Frequencies
GnomAD3 genomes AF: 0.238 AC: 19475AN: 81941Hom.: 2002 Cov.: 10 show subpopulations
GnomAD3 genomes
AF:
AC:
19475
AN:
81941
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:
GnomAD2 exomes AF: 0.0572 AC: 2955AN: 51637 AF XY: 0.00619 show subpopulations
GnomAD2 exomes
AF:
AC:
2955
AN:
51637
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0977 AC: 47800AN: 489004Hom.: 43 Cov.: 0 AF XY: 0.00185 AC XY: 222AN XY: 119990 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
47800
AN:
489004
Hom.:
Cov.:
0
AF XY:
AC XY:
222
AN XY:
119990
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1260
AN:
12242
American (AMR)
AF:
AC:
1320
AN:
18454
Ashkenazi Jewish (ASJ)
AF:
AC:
853
AN:
11698
East Asian (EAS)
AF:
AC:
793
AN:
23663
South Asian (SAS)
AF:
AC:
1637
AN:
25145
European-Finnish (FIN)
AF:
AC:
2800
AN:
29130
Middle Eastern (MID)
AF:
AC:
143
AN:
1958
European-Non Finnish (NFE)
AF:
AC:
36684
AN:
342730
Other (OTH)
AF:
AC:
2310
AN:
23984
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.381
Heterozygous variant carriers
0
2166
4332
6499
8665
10831
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
1156
2312
3468
4624
5780
<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 AF: 0.238 AC: 19483AN: 81926Hom.: 2006 Cov.: 10 AF XY: 0.158 AC XY: 2707AN XY: 17142 show subpopulations
GnomAD4 genome
AF:
AC:
19483
AN:
81926
Hom.:
Cov.:
10
AF XY:
AC XY:
2707
AN XY:
17142
show subpopulations
African (AFR)
AF:
AC:
4929
AN:
22308
American (AMR)
AF:
AC:
1541
AN:
7103
Ashkenazi Jewish (ASJ)
AF:
AC:
466
AN:
2101
East Asian (EAS)
AF:
AC:
139
AN:
2610
South Asian (SAS)
AF:
AC:
362
AN:
1527
European-Finnish (FIN)
AF:
AC:
387
AN:
2169
Middle Eastern (MID)
AF:
AC:
47
AN:
161
European-Non Finnish (NFE)
AF:
AC:
11263
AN:
42315
Other (OTH)
AF:
AC:
250
AN:
1077
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.515
Heterozygous variant carriers
0
536
1072
1608
2144
2680
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
184
368
552
736
920
<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.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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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