chr2-8730782-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_020738.4(KIDINS220):c.5254C>T(p.Leu1752Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,614,098 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L1752R) has been classified as Uncertain significance.
Frequency
Consequence
NM_020738.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIDINS220 | NM_020738.4 | c.5254C>T | p.Leu1752Phe | missense_variant | 30/30 | ENST00000256707.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIDINS220 | ENST00000256707.8 | c.5254C>T | p.Leu1752Phe | missense_variant | 30/30 | 1 | NM_020738.4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461892Hom.: 0 Cov.: 37 AF XY: 0.00000963 AC XY: 7AN XY: 727246
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.5254C>T (p.L1752F) alteration is located in exon 30 (coding exon 29) of the KIDINS220 gene. This alteration results from a C to T substitution at nucleotide position 5254, causing the leucine (L) at amino acid position 1752 to be replaced by a phenylalanine (F). 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