12-119690350-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001206999.2(CIT):c.5987G>A(p.Ser1996Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000814 in 1,598,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001206999.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000131 AC: 3AN: 228312Hom.: 0 AF XY: 0.00000797 AC XY: 1AN XY: 125532
GnomAD4 exome AF: 0.00000830 AC: 12AN: 1445822Hom.: 0 Cov.: 31 AF XY: 0.00000973 AC XY: 7AN XY: 719690
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74344
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.5987G>A (p.S1996N) alteration is located in exon 47 (coding exon 46) of the CIT gene. This alteration results from a G to A substitution at nucleotide position 5987, causing the serine (S) at amino acid position 1996 to be replaced by an asparagine (N). 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