17-7614523-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004860.4(FXR2):c.10C>G(p.Leu4Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000523 in 1,339,486 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004860.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FXR2 | NM_004860.4 | c.10C>G | p.Leu4Val | missense_variant | Exon 1 of 17 | ENST00000250113.12 | NP_004851.2 | |
FXR2 | XM_047437106.1 | c.10C>G | p.Leu4Val | missense_variant | Exon 1 of 17 | XP_047293062.1 | ||
SHBG | NM_001289114.2 | c.-62+412G>C | intron_variant | Intron 1 of 7 | NP_001276043.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151960Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.0000102 AC: 1AN: 98428Hom.: 0 AF XY: 0.0000178 AC XY: 1AN XY: 56210
GnomAD4 exome AF: 0.00000523 AC: 7AN: 1339486Hom.: 0 Cov.: 30 AF XY: 0.00000759 AC XY: 5AN XY: 659070
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151960Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74212
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.10C>G (p.L4V) alteration is located in exon 1 (coding exon 1) of the FXR2 gene. This alteration results from a C to G substitution at nucleotide position 10, causing the leucine (L) at amino acid position 4 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at