rs146907470
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001368397.1(FRMPD4):c.2903C>T(p.Ser968Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000603 in 1,210,032 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 24 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001368397.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FRMPD4 | NM_001368397.1 | c.2903C>T | p.Ser968Leu | missense_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.2903C>T | p.Ser968Leu | missense_variant | 16/17 | NM_001368397.1 | ENSP00000502607.1 |
Frequencies
GnomAD3 genomes AF: 0.0000622 AC: 7AN: 112552Hom.: 0 Cov.: 23 AF XY: 0.0000288 AC XY: 1AN XY: 34706
GnomAD3 exomes AF: 0.0000601 AC: 11AN: 183105Hom.: 0 AF XY: 0.0000739 AC XY: 5AN XY: 67625
GnomAD4 exome AF: 0.0000601 AC: 66AN: 1097426Hom.: 0 Cov.: 32 AF XY: 0.0000634 AC XY: 23AN XY: 362790
GnomAD4 genome AF: 0.0000622 AC: 7AN: 112606Hom.: 0 Cov.: 23 AF XY: 0.0000288 AC XY: 1AN XY: 34770
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 16, 2014 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at