chr1-109757060-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_133181.4(EPS8L3):āc.1075A>Gā(p.Ser359Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_133181.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPS8L3 | NM_133181.4 | c.1075A>G | p.Ser359Gly | missense_variant | 12/19 | ENST00000361965.9 | NP_573444.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPS8L3 | ENST00000361965.9 | c.1075A>G | p.Ser359Gly | missense_variant | 12/19 | 1 | NM_133181.4 | ENSP00000355255 | P4 | |
ENST00000431955.1 | n.628-18012T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251424Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135876
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727242
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.1078A>G (p.S360G) alteration is located in exon 12 (coding exon 11) of the EPS8L3 gene. This alteration results from a A to G substitution at nucleotide position 1078, causing the serine (S) at amino acid position 360 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