chr8-9008027-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_153332.4(ERI1):c.166T>C(p.Ser56Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,533,610 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_153332.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERI1 | NM_153332.4 | c.166T>C | p.Ser56Pro | missense_variant | 2/7 | ENST00000250263.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERI1 | ENST00000250263.8 | c.166T>C | p.Ser56Pro | missense_variant | 2/7 | 1 | NM_153332.4 | P1 | |
ERI1 | ENST00000519292.5 | c.166T>C | p.Ser56Pro | missense_variant | 2/8 | 2 | P1 | ||
ERI1 | ENST00000520684.5 | c.166T>C | p.Ser56Pro | missense_variant, NMD_transcript_variant | 2/6 | 5 | |||
ERI1 | ENST00000521844.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000904 AC: 122AN: 134938Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.000693 AC: 174AN: 251090Hom.: 0 AF XY: 0.000656 AC XY: 89AN XY: 135726
GnomAD4 exome AF: 0.00124 AC: 1735AN: 1398578Hom.: 0 Cov.: 35 AF XY: 0.00123 AC XY: 857AN XY: 694542
GnomAD4 genome ? AF: 0.000911 AC: 123AN: 135032Hom.: 0 Cov.: 28 AF XY: 0.000810 AC XY: 52AN XY: 64188
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.166T>C (p.S56P) alteration is located in exon 2 (coding exon 2) of the ERI1 gene. This alteration results from a T to C substitution at nucleotide position 166, causing the serine (S) at amino acid position 56 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
ERI1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 16, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at