chr14-24632975-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004131.6(GZMB):c.143G>A(p.Arg48Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004131.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GZMB | NM_004131.6 | c.143G>A | p.Arg48Lys | missense_variant | 2/5 | ENST00000216341.9 | |
GZMB | NM_001346011.2 | c.107G>A | p.Arg36Lys | missense_variant | 2/5 | ||
GZMB | NR_144343.2 | n.173G>A | non_coding_transcript_exon_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GZMB | ENST00000216341.9 | c.143G>A | p.Arg48Lys | missense_variant | 2/5 | 1 | NM_004131.6 | P2 | |
ENST00000555300.1 | n.177+9849C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251068Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135666
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461718Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727154
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | The c.143G>A (p.R48K) alteration is located in exon 2 (coding exon 2) of the GZMB gene. This alteration results from a G to A substitution at nucleotide position 143, causing the arginine (R) at amino acid position 48 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