12-104304203-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001008394.3(EID3):c.269C>T(p.Ala90Val) variant causes a missense change. The variant allele was found at a frequency of 0.000026 in 1,613,946 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_001008394.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EID3 | NM_001008394.3 | c.269C>T | p.Ala90Val | missense_variant | Exon 1 of 1 | ENST00000527879.2 | NP_001008395.1 | |
TXNRD1 | NM_001093771.3 | c.415-7087C>T | intron_variant | Intron 4 of 16 | ENST00000525566.6 | NP_001087240.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EID3 | ENST00000527879.2 | c.269C>T | p.Ala90Val | missense_variant | Exon 1 of 1 | 6 | NM_001008394.3 | ENSP00000435619.1 | ||
TXNRD1 | ENST00000525566.6 | c.415-7087C>T | intron_variant | Intron 4 of 16 | 1 | NM_001093771.3 | ENSP00000434516.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249300Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135248
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461710Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 727138
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.269C>T (p.A90V) alteration is located in exon 1 (coding exon 1) of the EID3 gene. This alteration results from a C to T substitution at nucleotide position 269, causing the alanine (A) at amino acid position 90 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