NM_004826.4:c.2166G>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_004826.4(ECEL1):c.2166G>A(p.Lys722Lys) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000514 in 1,613,838 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 Likely benign (★).
Frequency
Consequence
NM_004826.4 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.2166G>A | p.Lys722Lys | synonymous_variant | Exon 17 of 18 | ENST00000304546.6 | NP_004817.2 | |
ECEL1 | NM_001290787.2 | c.2160G>A | p.Lys720Lys | synonymous_variant | Exon 17 of 18 | NP_001277716.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.2166G>A | p.Lys722Lys | synonymous_variant | Exon 17 of 18 | 1 | NM_004826.4 | ENSP00000302051.1 | ||
ECEL1 | ENST00000409941.1 | c.2160G>A | p.Lys720Lys | synonymous_variant | Exon 16 of 17 | 1 | ENSP00000386333.1 | |||
ECEL1 | ENST00000411860.5 | c.345G>A | p.Lys115Lys | synonymous_variant | Exon 5 of 6 | 3 | ENSP00000412683.1 | |||
ECEL1 | ENST00000482346.1 | n.2477G>A | non_coding_transcript_exon_variant | Exon 16 of 17 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251124Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135806
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461616Hom.: 0 Cov.: 35 AF XY: 0.0000440 AC XY: 32AN XY: 727118
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
ECEL1-related disorder Benign:1
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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at