rs3177253
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_206836.3(ECI2):c.141G>T(p.Met47Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M47V) has been classified as Likely benign.
Frequency
Consequence
NM_206836.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECI2 | NM_206836.3 | c.141G>T | p.Met47Ile | missense_variant | 2/10 | ENST00000380118.8 | |
ECI2 | NM_001166010.2 | c.51G>T | p.Met17Ile | missense_variant | 2/10 | ||
ECI2 | NM_006117.3 | c.51G>T | p.Met17Ile | missense_variant | 2/10 | ||
ECI2 | NR_028588.2 | n.146G>T | non_coding_transcript_exon_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECI2 | ENST00000380118.8 | c.141G>T | p.Met47Ile | missense_variant | 2/10 | 1 | NM_206836.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250752Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135560
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461568Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727070
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at