chr6-61894801-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152688.4(KHDRBS2):c.644C>G(p.Pro215Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,612,208 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P215T) has been classified as Uncertain significance.
Frequency
Consequence
NM_152688.4 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 |
---|---|---|---|---|---|---|---|
KHDRBS2 | NM_152688.4 | c.644C>G | p.Pro215Arg | missense_variant | 6/9 | ENST00000281156.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KHDRBS2 | ENST00000281156.5 | c.644C>G | p.Pro215Arg | missense_variant | 6/9 | 1 | NM_152688.4 | P1 | |
KHDRBS2 | ENST00000675091.1 | c.644C>G | p.Pro215Arg | missense_variant, NMD_transcript_variant | 6/10 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152022Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248184Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134312
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1460186Hom.: 0 Cov.: 31 AF XY: 0.0000592 AC XY: 43AN XY: 726284
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152022Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74254
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.644C>G (p.P215R) alteration is located in exon 6 (coding exon 6) of the KHDRBS2 gene. This alteration results from a C to G substitution at nucleotide position 644, causing the proline (P) at amino acid position 215 to be replaced by an arginine (R). 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