12-92802632-T-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003566.4(EEA1):āc.2442A>Cā(p.Gln814His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000028 in 1,605,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003566.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEA1 | NM_003566.4 | c.2442A>C | p.Gln814His | missense_variant | 19/29 | ENST00000322349.13 | |
EEA1 | XM_011538814.3 | c.2568A>C | p.Gln856His | missense_variant | 20/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEA1 | ENST00000322349.13 | c.2442A>C | p.Gln814His | missense_variant | 19/29 | 1 | NM_003566.4 | P1 | |
EEA1 | ENST00000418984.7 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000373 AC: 9AN: 241200Hom.: 0 AF XY: 0.0000307 AC XY: 4AN XY: 130438
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1453268Hom.: 0 Cov.: 30 AF XY: 0.0000125 AC XY: 9AN XY: 722642
GnomAD4 genome AF: 0.000151 AC: 23AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2021 | The c.2442A>C (p.Q814H) alteration is located in exon 19 (coding exon 19) of the EEA1 gene. This alteration results from a A to C substitution at nucleotide position 2442, causing the glutamine (Q) at amino acid position 814 to be replaced by a histidine (H). 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