19-10554003-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_023008.5(KRI1):c.2060G>A(p.Arg687His) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,612,700 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023008.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRI1 | NM_023008.5 | c.2060G>A | p.Arg687His | missense_variant | Exon 19 of 19 | ENST00000312962.12 | NP_075384.4 | |
KRI1 | XM_047439232.1 | c.2066G>A | p.Arg689His | missense_variant | Exon 18 of 18 | XP_047295188.1 | ||
KRI1 | XM_011528190.3 | c.1724G>A | p.Arg575His | missense_variant | Exon 18 of 18 | XP_011526492.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249846Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135262
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460494Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 726416
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2078G>A (p.R693H) alteration is located in exon 19 (coding exon 19) of the KRI1 gene. This alteration results from a G to A substitution at nucleotide position 2078, causing the arginine (R) at amino acid position 693 to be replaced by a histidine (H). 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