chr2-142885488-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The NM_003937.3(KYNU):c.121C>T(p.His41Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. H41H) has been classified as Benign.
Frequency
Consequence
NM_003937.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KYNU | NM_003937.3 | c.121C>T | p.His41Tyr | missense_variant | 2/14 | ENST00000264170.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KYNU | ENST00000264170.9 | c.121C>T | p.His41Tyr | missense_variant | 2/14 | 1 | NM_003937.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000690 AC: 105AN: 152142Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000155 AC: 39AN: 251472Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135916
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461718Hom.: 0 Cov.: 31 AF XY: 0.0000509 AC XY: 37AN XY: 727138
GnomAD4 genome AF: 0.000690 AC: 105AN: 152260Hom.: 0 Cov.: 29 AF XY: 0.000631 AC XY: 47AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 02, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at