13-106493117-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_004093.4(EFNB2):c.925G>A(p.Gly309Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000285 in 1,614,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004093.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFNB2 | NM_004093.4 | c.925G>A | p.Gly309Arg | missense_variant | Exon 5 of 5 | ENST00000646441.1 | NP_004084.1 | |
EFNB2 | NM_001372056.1 | c.832G>A | p.Gly278Arg | missense_variant | Exon 4 of 4 | NP_001358985.1 | ||
EFNB2 | NM_001372057.1 | c.811G>A | p.Gly271Arg | missense_variant | Exon 4 of 4 | NP_001358986.1 | ||
EFNB2 | XM_017020406.3 | c.931G>A | p.Gly311Arg | missense_variant | Exon 5 of 5 | XP_016875895.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251302Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135822
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461710Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727160
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.925G>A (p.G309R) alteration is located in exon 5 (coding exon 5) of the EFNB2 gene. This alteration results from a G to A substitution at nucleotide position 925, causing the glycine (G) at amino acid position 309 to be replaced by an arginine (R). 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