rs76735188
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004826.4(ECEL1):c.967-7C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,613,230 control chromosomes in the GnomAD database, including 155 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004826.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.967-7C>G | splice_region_variant, intron_variant | Intron 4 of 17 | ENST00000304546.6 | NP_004817.2 | ||
ECEL1 | NM_001290787.2 | c.967-7C>G | splice_region_variant, intron_variant | Intron 4 of 17 | NP_001277716.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.967-7C>G | splice_region_variant, intron_variant | Intron 4 of 17 | 1 | NM_004826.4 | ENSP00000302051.1 | |||
ECEL1 | ENST00000409941.1 | c.967-7C>G | splice_region_variant, intron_variant | Intron 3 of 16 | 1 | ENSP00000386333.1 | ||||
ECEL1 | ENST00000482346.1 | n.1278-7C>G | splice_region_variant, intron_variant | Intron 3 of 16 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00880 AC: 1340AN: 152200Hom.: 12 Cov.: 34
GnomAD3 exomes AF: 0.00876 AC: 2196AN: 250802Hom.: 17 AF XY: 0.00865 AC XY: 1173AN XY: 135590
GnomAD4 exome AF: 0.0128 AC: 18701AN: 1460912Hom.: 143 Cov.: 60 AF XY: 0.0124 AC XY: 9006AN XY: 726782
GnomAD4 genome AF: 0.00880 AC: 1341AN: 152318Hom.: 12 Cov.: 34 AF XY: 0.00863 AC XY: 643AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:6
ECEL1: BP4, BS1, BS2 -
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not specified Benign:3
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at