chr19-16520850-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006387.6(CHERP):c.2177G>A(p.Arg726Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000322 in 1,461,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006387.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHERP | NM_006387.6 | c.2177G>A | p.Arg726Lys | missense_variant | Exon 13 of 17 | ENST00000546361.7 | NP_006378.3 | |
C19orf44 | NM_032207.4 | c.*797C>T | 3_prime_UTR_variant | Exon 9 of 9 | ENST00000221671.8 | NP_115583.1 | ||
C19orf44 | XM_006722920.5 | c.*797C>T | 3_prime_UTR_variant | Exon 8 of 8 | XP_006722983.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHERP | ENST00000546361.7 | c.2177G>A | p.Arg726Lys | missense_variant | Exon 13 of 17 | 1 | NM_006387.6 | ENSP00000439856.2 | ||
C19orf44 | ENST00000221671.8 | c.*797C>T | 3_prime_UTR_variant | Exon 9 of 9 | 2 | NM_032207.4 | ENSP00000221671.2 | |||
ENSG00000141979 | ENST00000409035.1 | n.*194-1498G>A | intron_variant | Intron 6 of 11 | 2 | ENSP00000386951.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249222Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135260
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461578Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727122
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2177G>A (p.R726K) alteration is located in exon 13 (coding exon 13) of the CHERP gene. This alteration results from a G to A substitution at nucleotide position 2177, causing the arginine (R) at amino acid position 726 to be replaced by a lysine (K). 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