rs2080117
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001329101.2(KLRG1):c.-155-6461C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,020 control chromosomes in the GnomAD database, including 10,568 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.35 ( 10568 hom., cov: 31)
Consequence
KLRG1
NM_001329101.2 intron
NM_001329101.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.199
Genes affected
KLRG1 (HGNC:6380): (killer cell lectin like receptor G1) Natural killer (NK) cells are lymphocytes that can mediate lysis of certain tumor cells and virus-infected cells without previous activation. They can also regulate specific humoral and cell-mediated immunity. The protein encoded by this gene belongs to the killer cell lectin-like receptor (KLR) family, which is a group of transmembrane proteins preferentially expressed in NK cells. Studies in mice suggested that the expression of this gene may be regulated by MHC class I molecules. [provided by RefSeq, Jun 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLRG1 | NM_001329101.2 | c.-155-6461C>T | intron_variant | ||||
KLRG1 | NM_001329102.2 | c.-289-4467C>T | intron_variant | ||||
KLRG1 | NM_001329103.2 | c.-155-6461C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLRG1 | ENST00000539240.5 | c.-155-6461C>T | intron_variant | 3 | |||||
KLRG1 | ENST00000538029.1 | n.113-23230C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
KLRG1 | ENST00000541957.1 | n.248-4467C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
KLRG1 | ENST00000544226.5 | n.131-6461C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.347 AC: 52714AN: 151902Hom.: 10564 Cov.: 31
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.347 AC: 52723AN: 152020Hom.: 10568 Cov.: 31 AF XY: 0.350 AC XY: 25982AN XY: 74298
GnomAD4 genome
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1412
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at