rs41303149
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_001368397.1(FRMPD4):c.3937C>A(p.Arg1313=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,198,771 control chromosomes in the GnomAD database, including 8 homozygotes. There are 742 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001368397.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FRMPD4 | NM_001368397.1 | c.3937C>A | p.Arg1313= | synonymous_variant | 16/17 | ENST00000675598.1 | NP_001355326.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRMPD4 | ENST00000675598.1 | c.3937C>A | p.Arg1313= | synonymous_variant | 16/17 | NM_001368397.1 | ENSP00000502607 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00147 AC: 165AN: 111968Hom.: 0 Cov.: 23 AF XY: 0.00135 AC XY: 46AN XY: 34140
GnomAD3 exomes AF: 0.00184 AC: 330AN: 179217Hom.: 0 AF XY: 0.00176 AC XY: 115AN XY: 65499
GnomAD4 exome AF: 0.00195 AC: 2123AN: 1086750Hom.: 8 Cov.: 29 AF XY: 0.00197 AC XY: 696AN XY: 352788
GnomAD4 genome AF: 0.00147 AC: 165AN: 112021Hom.: 0 Cov.: 23 AF XY: 0.00134 AC XY: 46AN XY: 34203
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 20, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 29, 2015 | - - |
Autism, susceptibility to, X-linked 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Human Genetics, Inc, Center for Human Genetics, Inc | Nov 01, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at