19-11513839-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_016581.5(ECSIT):c.479G>A(p.Cys160Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016581.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECSIT | NM_016581.5 | c.479G>A | p.Cys160Tyr | missense_variant | Exon 3 of 8 | ENST00000270517.12 | NP_057665.2 | |
ECSIT | NM_001142464.3 | c.479G>A | p.Cys160Tyr | missense_variant | Exon 3 of 7 | NP_001135936.1 | ||
ECSIT | NM_001243204.2 | c.479G>A | p.Cys160Tyr | missense_variant | Exon 3 of 8 | NP_001230133.1 | ||
ECSIT | NM_001142465.3 | c.96+5236G>A | intron_variant | Intron 2 of 5 | NP_001135937.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251380Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135874
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461872Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727238
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.479G>A (p.C160Y) alteration is located in exon 3 (coding exon 2) of the ECSIT gene. This alteration results from a G to A substitution at nucleotide position 479, causing the cysteine (C) at amino acid position 160 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at