13-106493414-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004093.4(EFNB2):c.628G>A(p.Gly210Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000416 in 1,612,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFNB2 | NM_004093.4 | c.628G>A | p.Gly210Ser | missense_variant | Exon 5 of 5 | ENST00000646441.1 | NP_004084.1 | |
EFNB2 | NM_001372056.1 | c.535G>A | p.Gly179Ser | missense_variant | Exon 4 of 4 | NP_001358985.1 | ||
EFNB2 | NM_001372057.1 | c.514G>A | p.Gly172Ser | missense_variant | Exon 4 of 4 | NP_001358986.1 | ||
EFNB2 | XM_017020406.3 | c.634G>A | p.Gly212Ser | missense_variant | Exon 5 of 5 | XP_016875895.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249124Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134576
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1459992Hom.: 0 Cov.: 30 AF XY: 0.0000386 AC XY: 28AN XY: 726084
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.628G>A (p.G210S) 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 628, causing the glycine (G) at amino acid position 210 to be replaced by a serine (S). 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