chr6-149945390-T-C

Variant names:

• chr6-149945390-T-C
• rs767264674
• NM_025217.4:c.167T>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_025217.4(ULBP2):​c.167T>C​(p.Val56Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V56E) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: ULBP2 NM_025217.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.39
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ULBP2	NM_025217.4	c.167T>C	p.Val56Ala	missense_variant	Exon 2 of 5	ENST00000367351.4	NP_079493.1
ULBP2	XM_047419377.1	c.167T>C	p.Val56Ala	missense_variant	Exon 2 of 4		XP_047275333.1
ULBP2	XM_017011321.2	c.167T>C	p.Val56Ala	missense_variant	Exon 2 of 4		XP_016866810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ULBP2	ENST00000367351.4	c.167T>C	p.Val56Ala	missense_variant	Exon 2 of 5	1	NM_025217.4	ENSP00000356320.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jul 17, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.167T>C (p.V56A) alteration is located in exon 2 (coding exon 2) of the ULBP2 gene. This alteration results from a T to C substitution at nucleotide position 167, causing the valine (V) at amino acid position 56 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.37
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	21
DANN	Benign	0.93
DEOGEN2	Benign	0.13	T
Eigen	Benign	-0.22
Eigen_PC	Benign	-0.50
FATHMM_MKL	Benign	0.045	N
LIST_S2	Benign	0.62	T
M_CAP	Benign	0.0019	T
MetaRNN	Uncertain	0.69	D
MetaSVM	Benign	-1.1	T
PhyloP100		2.4
PrimateAI	Benign	0.34	T
PROVEAN	Uncertain	-3.7	D
REVEL	Benign	0.075
Sift	Uncertain	0.022	D
Sift4G	Uncertain	0.026	D
Polyphen		0.95	P
Vest4		0.36
MutPred		0.79		Loss of sheet (P = 0.0817);
MVP		0.23
MPC		2.5
ClinPred		0.40	T
GERP RS		2.2
Varity_R		0.26
gMVP		0.25
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs767264674; hg19: chr6-150266526;