19-39532447-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152361.3(EID2B):c.356G>A(p.Arg119Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152361.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EID2B | NM_152361.3 | c.356G>A | p.Arg119Lys | missense_variant | 1/1 | ENST00000326282.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EID2B | ENST00000326282.5 | c.356G>A | p.Arg119Lys | missense_variant | 1/1 | NM_152361.3 | P1 | ||
ENST00000594676.1 | n.36C>T | non_coding_transcript_exon_variant | 1/3 | 4 | |||||
EID2B | ENST00000601837.1 | n.104+293G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152274Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251062Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135864
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461812Hom.: 0 Cov.: 29 AF XY: 0.00000550 AC XY: 4AN XY: 727206
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 13, 2023 | The c.356G>A (p.R119K) alteration is located in exon 1 (coding exon 1) of the EID2B gene. This alteration results from a G to A substitution at nucleotide position 356, causing the arginine (R) at amino acid position 119 to be replaced by a lysine (K). 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