rs141146885
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001397.3(ECE1):c.1385G>A(p.Ser462Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00461 in 1,614,136 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001397.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECE1 | NM_001397.3 | c.1385G>A | p.Ser462Asn | missense_variant | 11/19 | ENST00000374893.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECE1 | ENST00000374893.11 | c.1385G>A | p.Ser462Asn | missense_variant | 11/19 | 1 | NM_001397.3 |
Frequencies
GnomAD3 genomes ? AF: 0.00335 AC: 510AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00297 AC: 748AN: 251432Hom.: 4 AF XY: 0.00313 AC XY: 426AN XY: 135892
GnomAD4 exome AF: 0.00474 AC: 6929AN: 1461778Hom.: 22 Cov.: 31 AF XY: 0.00460 AC XY: 3345AN XY: 727188
GnomAD4 genome ? AF: 0.00335 AC: 510AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.00275 AC XY: 205AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 08, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at