NM_004826.4:c.1995C>T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_004826.4(ECEL1):c.1995C>T(p.Asn665Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 1,564,584 control chromosomes in the GnomAD database, including 443 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004826.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.1995C>T | p.Asn665Asn | synonymous_variant | Exon 15 of 18 | ENST00000304546.6 | NP_004817.2 | |
ECEL1 | NM_001290787.2 | c.1989C>T | p.Asn663Asn | synonymous_variant | Exon 15 of 18 | NP_001277716.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.1995C>T | p.Asn665Asn | synonymous_variant | Exon 15 of 18 | 1 | NM_004826.4 | ENSP00000302051.1 | ||
ECEL1 | ENST00000409941.1 | c.1989C>T | p.Asn663Asn | synonymous_variant | Exon 14 of 17 | 1 | ENSP00000386333.1 | |||
ECEL1 | ENST00000411860.5 | c.235-338C>T | intron_variant | Intron 3 of 5 | 3 | ENSP00000412683.1 | ||||
ECEL1 | ENST00000482346.1 | n.2306C>T | non_coding_transcript_exon_variant | Exon 14 of 17 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0157 AC: 2386AN: 152228Hom.: 40 Cov.: 34
GnomAD3 exomes AF: 0.0154 AC: 2669AN: 172986Hom.: 38 AF XY: 0.0152 AC XY: 1396AN XY: 91950
GnomAD4 exome AF: 0.0218 AC: 30786AN: 1412238Hom.: 404 Cov.: 33 AF XY: 0.0214 AC XY: 14917AN XY: 697888
GnomAD4 genome AF: 0.0157 AC: 2385AN: 152346Hom.: 39 Cov.: 34 AF XY: 0.0150 AC XY: 1115AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at