chr2-95382450-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_013434.5(KCNIP3):c.629C>T(p.Ala210Val) variant causes a missense change. The variant allele was found at a frequency of 0.00015 in 1,608,842 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict 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. A210P) has been classified as Uncertain significance.
Frequency
Consequence
NM_013434.5 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 |
---|---|---|---|---|---|---|---|
KCNIP3 | NM_013434.5 | c.629C>T | p.Ala210Val | missense_variant | 7/9 | ENST00000295225.10 | |
KCNIP3 | NM_001034914.2 | c.551C>T | p.Ala184Val | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNIP3 | ENST00000295225.10 | c.629C>T | p.Ala210Val | missense_variant | 7/9 | 1 | NM_013434.5 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000650 AC: 16AN: 245986Hom.: 0 AF XY: 0.0000674 AC XY: 9AN XY: 133566
GnomAD4 exome AF: 0.000159 AC: 231AN: 1456676Hom.: 0 Cov.: 30 AF XY: 0.000149 AC XY: 108AN XY: 724724
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2023 | The c.629C>T (p.A210V) alteration is located in exon 7 (coding exon 7) of the KCNIP3 gene. This alteration results from a C to T substitution at nucleotide position 629, causing the alanine (A) at amino acid position 210 to be replaced by a valine (V). 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