3-50610395-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000443053.6(CISH):c.49G>A(p.Ala17Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,551,442 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000443053.6 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CISH | NM_145071.4 | c.20+1236G>A | intron_variant | ENST00000348721.4 | |||
CISH | NM_013324.7 | c.49G>A | p.Ala17Thr | missense_variant | 2/4 | ||
CISH | XM_047447398.1 | c.49G>A | p.Ala17Thr | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CISH | ENST00000443053.6 | c.49G>A | p.Ala17Thr | missense_variant | 2/4 | 1 | |||
CISH | ENST00000348721.4 | c.20+1236G>A | intron_variant | 1 | NM_145071.4 | P1 | |||
CISH | ENST00000491847.1 | n.1367G>A | non_coding_transcript_exon_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000383 AC: 6AN: 156584Hom.: 0 AF XY: 0.0000603 AC XY: 5AN XY: 82970
GnomAD4 exome AF: 0.00000858 AC: 12AN: 1399236Hom.: 0 Cov.: 29 AF XY: 0.0000145 AC XY: 10AN XY: 690130
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 30, 2023 | The c.49G>A (p.A17T) alteration is located in exon 2 (coding exon 1) of the CISH gene. This alteration results from a G to A substitution at nucleotide position 49, causing the alanine (A) at amino acid position 17 to be replaced by a threonine (T). 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