chr12-92778082-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003566.4(EEA1):c.3752G>A(p.Gly1251Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000329 in 1,613,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EEA1 | NM_003566.4 | c.3752G>A | p.Gly1251Asp | missense_variant | Exon 26 of 29 | ENST00000322349.13 | NP_003557.3 | |
EEA1 | XM_011538814.3 | c.3878G>A | p.Gly1293Asp | missense_variant | Exon 27 of 30 | XP_011537116.1 | ||
LOC124902984 | XR_007063407.1 | n.*146C>T | downstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151894Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251116Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135742
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461348Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 726988
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151894Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74194
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3752G>A (p.G1251D) alteration is located in exon 26 (coding exon 26) of the EEA1 gene. This alteration results from a G to A substitution at nucleotide position 3752, causing the glycine (G) at amino acid position 1251 to be replaced by an aspartic acid (D). 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