13-106493262-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_004093.4(EFNB2):c.780G>A(p.Ser260Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 1,614,152 control chromosomes in the GnomAD database, including 429 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_004093.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFNB2 | NM_004093.4 | c.780G>A | p.Ser260Ser | synonymous_variant | Exon 5 of 5 | ENST00000646441.1 | NP_004084.1 | |
EFNB2 | NM_001372056.1 | c.687G>A | p.Ser229Ser | synonymous_variant | Exon 4 of 4 | NP_001358985.1 | ||
EFNB2 | NM_001372057.1 | c.666G>A | p.Ser222Ser | synonymous_variant | Exon 4 of 4 | NP_001358986.1 | ||
EFNB2 | XM_017020406.3 | c.786G>A | p.Ser262Ser | synonymous_variant | Exon 5 of 5 | XP_016875895.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0166 AC: 2522AN: 152144Hom.: 28 Cov.: 33
GnomAD3 exomes AF: 0.0169 AC: 4247AN: 251464Hom.: 42 AF XY: 0.0170 AC XY: 2306AN XY: 135906
GnomAD4 exome AF: 0.0222 AC: 32397AN: 1461890Hom.: 401 Cov.: 30 AF XY: 0.0219 AC XY: 15902AN XY: 727246
GnomAD4 genome AF: 0.0166 AC: 2521AN: 152262Hom.: 28 Cov.: 33 AF XY: 0.0156 AC XY: 1159AN XY: 74456
ClinVar
Submissions by phenotype
EFNB2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at