chr2-8730821-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_020738.4(KIDINS220):c.5215C>T(p.Arg1739Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 1,614,100 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. R1739H) 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.5215C>T | p.Arg1739Cys | missense_variant | 30/30 | ENST00000256707.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIDINS220 | ENST00000256707.8 | c.5215C>T | p.Arg1739Cys | missense_variant | 30/30 | 1 | NM_020738.4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249576Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135406
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461886Hom.: 0 Cov.: 37 AF XY: 0.0000165 AC XY: 12AN XY: 727246
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2021 | The c.5215C>T (p.R1739C) 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 5215, causing the arginine (R) at amino acid position 1739 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
KIDINS220-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 23, 2023 | The KIDINS220 c.5215C>T variant is predicted to result in the amino acid substitution p.Arg1739Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0056% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-8870951-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at