chr6-31592893-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PP5BP4BS1_SupportingBS2_Supporting
The NM_147130.3(NCR3):c.-172G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 680,664 control chromosomes in the GnomAD database, including 294 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_147130.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NCR3 | ENST00000340027.10 | c.-172G>A | 5_prime_UTR_variant | Exon 1 of 4 | 1 | NM_147130.3 | ENSP00000342156.5 | |||
NCR3 | ENST00000376072.7 | c.-172G>A | 5_prime_UTR_variant | Exon 1 of 4 | 1 | ENSP00000365240.3 | ||||
NCR3 | ENST00000376073.8 | c.-172G>A | 5_prime_UTR_variant | Exon 1 of 4 | 1 | ENSP00000365241.4 | ||||
NCR3 | ENST00000491161.1 | n.67G>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0233 AC: 3540AN: 152066Hom.: 75 Cov.: 31
GnomAD4 exome AF: 0.0212 AC: 11182AN: 528480Hom.: 219 Cov.: 6 AF XY: 0.0200 AC XY: 5599AN XY: 280500
GnomAD4 genome AF: 0.0233 AC: 3539AN: 152184Hom.: 75 Cov.: 31 AF XY: 0.0212 AC XY: 1577AN XY: 74390
ClinVar
Submissions by phenotype
Malaria, severe, susceptibility to Pathogenic:1
CC is wild type in the Luo (Kenya) population, TT is homozygous mutant. TT increases susceptibility to longitudinal (over 36 months) falciparum malaria episodes in children less than 48 months of age. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at