chr12-92778163-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003566.4(EEA1):āc.3671A>Gā(p.Glu1224Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,611,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEA1 | NM_003566.4 | c.3671A>G | p.Glu1224Gly | missense_variant | 26/29 | ENST00000322349.13 | |
EEA1 | XM_011538814.3 | c.3797A>G | p.Glu1266Gly | missense_variant | 27/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEA1 | ENST00000322349.13 | c.3671A>G | p.Glu1224Gly | missense_variant | 26/29 | 1 | NM_003566.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248094Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133928
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1458982Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 725544
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.3671A>G (p.E1224G) alteration is located in exon 26 (coding exon 26) of the EEA1 gene. This alteration results from a A to G substitution at nucleotide position 3671, causing the glutamic acid (E) at amino acid position 1224 to be replaced by a glycine (G). 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