9-127945436-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001035254.3(EEIG1):c.848G>A(p.Arg283Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000014 in 1,566,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R283W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001035254.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EEIG1 | ENST00000373095.6 | c.848G>A | p.Arg283Gln | missense_variant | Exon 8 of 11 | 5 | NM_001035254.3 | ENSP00000362187.1 | ||
EEIG1 | ENST00000373084.8 | c.422G>A | p.Arg141Gln | missense_variant | Exon 5 of 8 | 1 | ENSP00000362176.4 | |||
EEIG1 | ENST00000300434.3 | n.532G>A | non_coding_transcript_exon_variant | Exon 3 of 6 | 1 | |||||
EEIG1 | ENST00000465821.5 | n.321G>A | non_coding_transcript_exon_variant | Exon 3 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000116 AC: 2AN: 171712Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 91984
GnomAD4 exome AF: 0.0000134 AC: 19AN: 1413930Hom.: 0 Cov.: 33 AF XY: 0.0000143 AC XY: 10AN XY: 699260
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.848G>A (p.R283Q) alteration is located in exon 8 (coding exon 8) of the FAM102A gene. This alteration results from a G to A substitution at nucleotide position 848, causing the arginine (R) at amino acid position 283 to be replaced by a glutamine (Q). 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