6-149945375-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025217.4(ULBP2):c.152C>T(p.Ala51Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,612,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025217.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ULBP2 | NM_025217.4 | c.152C>T | p.Ala51Val | missense_variant | Exon 2 of 5 | ENST00000367351.4 | NP_079493.1 | |
ULBP2 | XM_047419377.1 | c.152C>T | p.Ala51Val | missense_variant | Exon 2 of 4 | XP_047275333.1 | ||
ULBP2 | XM_017011321.2 | c.152C>T | p.Ala51Val | missense_variant | Exon 2 of 4 | XP_016866810.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000593 AC: 9AN: 151876Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250592Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135538
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1460630Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 726666
GnomAD4 genome AF: 0.0000592 AC: 9AN: 151992Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.152C>T (p.A51V) alteration is located in exon 2 (coding exon 2) of the ULBP2 gene. This alteration results from a C to T substitution at nucleotide position 152, causing the alanine (A) at amino acid position 51 to be replaced by a valine (V). 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