chr4-1022236-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001004356.3(FGFRL1):c.113G>A(p.Arg38Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000323 in 1,554,480 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R38R) has been classified as Likely benign.
Frequency
Consequence
NM_001004356.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGFRL1 | NM_001004356.3 | c.113G>A | p.Arg38Gln | missense_variant | 3/7 | ENST00000510644.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGFRL1 | ENST00000510644.6 | c.113G>A | p.Arg38Gln | missense_variant | 3/7 | 1 | NM_001004356.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152118Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000699 AC: 134AN: 191774Hom.: 0 AF XY: 0.000878 AC XY: 93AN XY: 105890
GnomAD4 exome AF: 0.000340 AC: 477AN: 1402246Hom.: 7 Cov.: 31 AF XY: 0.000482 AC XY: 333AN XY: 690544
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152234Hom.: 1 Cov.: 34 AF XY: 0.000242 AC XY: 18AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at