chr2-85694429-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBA1
The NM_006433.5(GNLY):c.11G>A(p.Trp4Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0045 in 1,614,064 control chromosomes in the GnomAD database, including 288 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.024 ( 141 hom., cov: 34)
Exomes 𝑓: 0.0025 ( 147 hom. )
Consequence
GNLY
NM_006433.5 stop_gained
NM_006433.5 stop_gained
Scores
7
Clinical Significance
Conservation
PhyloP100: 0.359
Genes affected
GNLY (HGNC:4414): (granulysin) The product of this gene is a member of the saposin-like protein (SAPLIP) family and is located in the cytotoxic granules of T cells, which are released upon antigen stimulation. This protein is present in cytotoxic granules of cytotoxic T lymphocytes and natural killer cells, and it has antimicrobial activity against M. tuberculosis and other organisms. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
PM4
?
Stoplost variant in NM_006433.5 Downstream stopcodon found after 165 codons.
BP6
?
Variant 2-85694429-G-A is Benign according to our data. Variant chr2-85694429-G-A is described in ClinVar as [Benign]. Clinvar id is 780828.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0812 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNLY | NM_006433.5 | c.11G>A | p.Trp4Ter | stop_gained | 1/5 | ENST00000263863.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNLY | ENST00000263863.9 | c.11G>A | p.Trp4Ter | stop_gained | 1/5 | 1 | NM_006433.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0240 AC: 3657AN: 152236Hom.: 140 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00643 AC: 1615AN: 250998Hom.: 65 AF XY: 0.00482 AC XY: 654AN XY: 135724
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GnomAD4 exome AF: 0.00247 AC: 3615AN: 1461708Hom.: 147 Cov.: 31 AF XY: 0.00210 AC XY: 1527AN XY: 727160
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GnomAD4 genome ? AF: 0.0240 AC: 3653AN: 152356Hom.: 141 Cov.: 34 AF XY: 0.0233 AC XY: 1737AN XY: 74500
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ESP6500AA
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357
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ClinVar
Significance: Benign
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, no assertion criteria provided | literature only | OMIM | Mar 09, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 20, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 28, 2020 | This variant is associated with the following publications: (PMID: 31642954) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
A;A;N
Vest4
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at