6-149946451-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_025217.4(ULBP2):c.429C>T(p.Phe143Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000038 ( 0 hom. )
Consequence
ULBP2
NM_025217.4 synonymous
NM_025217.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.756
Genes affected
ULBP2 (HGNC:14894): (UL16 binding protein 2) This gene encodes a major histocompatibility complex (MHC) class I-related molecule that binds to the NKG2D receptor on natural killer (NK) cells to trigger release of multiple cytokines and chemokines that in turn contribute to the recruitment and activation of NK cells. The encoded protein undergoes further processing to generate the mature protein that is either anchored to membrane via a glycosylphosphatidylinositol moiety, or secreted. Many malignant cells secrete the encoded protein to evade immunosurveillance by NK cells. This gene is located in a cluster of multiple MHC class I-related genes on chromosome 6. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 6-149946451-C-T is Benign according to our data. Variant chr6-149946451-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 747387.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ULBP2 | NM_025217.4 | c.429C>T | p.Phe143Phe | synonymous_variant | Exon 3 of 5 | ENST00000367351.4 | NP_079493.1 | |
ULBP2 | XM_047419377.1 | c.429C>T | p.Phe143Phe | synonymous_variant | Exon 3 of 4 | XP_047275333.1 | ||
ULBP2 | XM_017011321.2 | c.429C>T | p.Phe143Phe | synonymous_variant | Exon 3 of 4 | XP_016866810.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152108Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251494Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135922
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GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461890Hom.: 0 Cov.: 34 AF XY: 0.0000454 AC XY: 33AN XY: 727248
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152226Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74408
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 10, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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BayesDel_noAF
Benign
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DANN
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Splicing
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Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 32
Find out detailed SpliceAI scores and Pangolin per-transcript scores at